MII IG Onkologie DE v2025

There are no (further) constraints on this element

Element id

Observation.id

Short description

Logical id of this artifact

Definition

The logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes.

Comments

The only time that a resource does not have an id is when it is being submitted to the server using a create operation.

Data type

category

1..*

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.category

Short description

Classification of type of observation

Definition

A code that classifies the general type of observation being made.

Requirements

Used for filtering what observations are retrieved and displayed.

Comments

In addition to the required category valueset, this element allows various categorization schemes based on the owner’s definition of the category and effectively multiple categories can be used at once. The level of granularity is defined by the category concepts in the value set.

Data type

ObservationCategoryCodes (preferred)

Slicing

Unordered, Open, by coding(Value)

Slice based on the category.code pattern

Binding

Codes for high level observation categories.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
w5: FiveWs.class
rim: .outboundRelationship[typeCode="COMP].target[classCode="LIST", moodCode="EVN"].code

labCategory

1..1

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.category:labCategory

Short description

Classification of type of observation

Definition

A code that classifies the general type of observation being made.

Requirements

Used for filtering what observations are retrieved and displayed.

Comments

Data type

ObservationCategoryCodes (preferred)

Binding

Codes for high level observation categories.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
w5: FiveWs.class
rim: .outboundRelationship[typeCode="COMP].target[classCode="LIST", moodCode="EVN"].code

0..1

There are no (further) constraints on this element

Element id

Observation.category:labCategory.id

Short description

Unique id for inter-element referencing

Definition

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Data type

Mappings

rim: n/a

extension

0..*

There are no (further) constraints on this element

Element id

Observation.category:labCategory.extension

Short description

Additional content defined by implementations

Alternate names

extensions, user content

Definition

Comments

Data type

Slicing

Unordered, Open, by url(Value)

Extensions are always sliced by (at least) url

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

coding

1..*

CodingPattern

There are no (further) constraints on this element

Element id

Observation.category:labCategory.coding

Short description

Code defined by a terminology system

Definition

A reference to a code defined by a terminology system.

Requirements

Allows for alternative encodings within a code system, and translations to other code systems.

Comments

Codes may be defined very casually in enumerations, or code lists, up to very formal definitions such as SNOMED CT - see the HL7 v3 Core Principles for more information. Ordering of codings is undefined and SHALL NOT be used to infer meaning. Generally, at most only one of the coding values will be labeled as UserSelected = true.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Pattern

{
  "system": "http://terminology.hl7.org/CodeSystem/observation-category",
  "code": "laboratory"
}

Mappings

rim: n/a
v2: CE/CNE/CWE subset one of the sets of component 1-3 or 4-6
rim: CV
orim: fhir:Coding rdfs:subClassOf dt:CDCoding
v2: C*E.1-8, C*E.10-22
rim: union(., ./translation)
orim: fhir:CodeableConcept.coding rdfs:subPropertyOf dt:CD.coding

text

0..1

There are no (further) constraints on this element

Element id

Observation.category:labCategory.text

Short description

Plain text representation of the concept

Definition

A human language representation of the concept as seen/selected/uttered by the user who entered the data and/or which represents the intended meaning of the user.

Requirements

The codes from the terminologies do not always capture the correct meaning with all the nuances of the human using them, or sometimes there is no appropriate code at all. In these cases, the text is used to capture the full meaning of the source.

Comments

Very often the text is the same as a displayName of one of the codings.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: C*E.9. But note many systems use C*E.2 for this
rim: ./originalText[mediaType/code="text/plain"]/data
orim: fhir:CodeableConcept.text rdfs:subPropertyOf dt:CD.originalText

code

S Σ

1..1

CodeableConceptPattern

There are no (further) constraints on this element

Element id

Observation.code

Short description

69548-6

Alternate names

Name

Definition

Describes what was observed. Sometimes this is called the observation "name".

Requirements

Knowing what kind of observation is being made is essential to understanding the observation.

Comments

All code-value and, if present, component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

Data type

Binding

Codes identifying names of simple observations.

Reference(MII_PR_Onko_Diagnose_Primaertumor)

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Pattern

{
  "coding": [
    {
      "system": "http://loinc.org",
      "code": "69548-6"
    }
  ]
}

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
workflow: Event.code
w5: FiveWs.what[x]
sct-concept: < 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
v2: OBX-3
rim: code
sct-attr: 116680003 |Is a|

subject

S Σ C

1..1

Reference(Patient)

Element id

Observation.subject

Short description

Who and/or what the observation is about

Definition

The patient, or group of patients, location, or device this observation is about and into whose record the observation is placed. If the actual focus of the observation is different from the subject (or a sample of, part, or region of the subject), the focus element or the code itself specifies the actual focus of the observation.

Requirements

Observations have no value if you don't know who or what they're about.

Comments

One would expect this element to be a cardinality of 1..1. The only circumstance in which the subject can be missing is when the observation is made by a device that does not know the patient. In this case, the observation SHALL be matched to a patient through some context/channel matching technique, and at this point, the observation should be updated.

Data type

Reference(Patient)

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ref-1: SHALL have a contained resource if a local reference is provided
reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))

Mappings

rim: n/a
rim: The target of a resource reference is a RIM entry point (Act, Role, or Entity)
workflow: Event.subject
w5: FiveWs.subject[x]
v2: PID-3
rim: participation[typeCode=RTGT]
w5: FiveWs.subject

focus

S Σ C

0..*

Element id

Observation.focus

Short description

What the observation is about, when it is not about the subject of record

Definition

The actual focus of an observation when it is not the patient of record representing something or someone associated with the patient such as a spouse, parent, fetus, or donor. For example, fetus observations in a mother's record. The focus of an observation could also be an existing condition, an intervention, the subject's diet, another observation of the subject, or a body structure such as tumor or implanted device. An example use case would be using the Observation resource to capture whether the mother is trained to change her child's tracheostomy tube. In this example, the child is the patient of record and the mother is the focus.

Comments

Typically, an observation is made about the subject - a patient, or group of patients, location, or device - and the distinction between the subject and what is directly measured for an observation is specified in the observation code itself ( e.g., "Blood Glucose") and does not need to be represented separately using this element. Use specimen if a reference to a specimen is required. If a code is required instead of a resource use either bodysite for bodysites or the standard extension focusCode.

Data type

Reference(MII_PR_Onko_Diagnose_Primaertumor)

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ref-1: SHALL have a contained resource if a local reference is provided
reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))

Mappings

rim: n/a
rim: The target of a resource reference is a RIM entry point (Act, Role, or Entity)
w5: FiveWs.subject[x]
v2: OBX-3
rim: participation[typeCode=SBJ]
w5: FiveWs.subject

encounter

S Σ C

0..1

Reference(Encounter)

There are no (further) constraints on this element

Element id

Observation.encounter

Short description

Healthcare event during which this observation is made

Alternate names

Context

Definition

The healthcare event (e.g. a patient and healthcare provider interaction) during which this observation is made.

Requirements

For some observations it may be important to know the link between an observation and a particular encounter.

Comments

This will typically be the encounter the event occurred within, but some events may be initiated prior to or after the official completion of an encounter but still be tied to the context of the encounter (e.g. pre-admission laboratory tests).

Data type

Reference(Encounter)

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ref-1: SHALL have a contained resource if a local reference is provided
reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))

Mappings

rim: n/a
rim: The target of a resource reference is a RIM entry point (Act, Role, or Entity)
workflow: Event.context
w5: FiveWs.context
v2: PV1
rim: inboundRelationship[typeCode=COMP].source[classCode=ENC, moodCode=EVN]

effective[x]

0..1

There are no (further) constraints on this element

Element id

Observation.effective[x]

Short description

Clinically relevant time/time-period for observation

Alternate names

Occurrence

Definition

The time or time-period the observed value is asserted as being true. For biological subjects - e.g. human patients - this is usually called the "physiologically relevant time". This is usually either the time of the procedure or of specimen collection, but very often the source of the date/time is not known, only the date/time itself.

Requirements

Knowing when an observation was deemed true is important to its relevance as well as determining trends.

Comments

At least a date should be present unless this observation is a historical report. For recording imprecise or "fuzzy" times (For example, a blood glucose measurement taken "after breakfast") use the Timing datatype which allow the measurement to be tied to regular life events.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
workflow: Event.occurrence[x]
w5: FiveWs.done[x]
v2: OBX-14, and/or OBX-19 after v2.4 (depends on who observation made)
rim: effectiveTime

effectiveDateTime

There are no (further) constraints on this element

Data type

effectiveInstant

There are no (further) constraints on this element

Data type

effectivePeriod

There are no (further) constraints on this element

Data type

effectiveTiming

Timing

There are no (further) constraints on this element

Data type

Timing

issued

0..1

There are no (further) constraints on this element

Element id

Observation.issued

Short description

Date/Time this version was made available

Definition

The date and time this version of the observation was made available to providers, typically after the results have been reviewed and verified.

Comments

For Observations that don’t require review and verification, it may be the same as the lastUpdated time of the resource itself. For Observations that do require review and verification for certain updates, it might not be the same as the lastUpdated time of the resource itself due to a non-clinically significant update that doesn’t require the new version to be reviewed and verified again.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
w5: FiveWs.recorded
v2: OBR.22 (or MSH.7), or perhaps OBX-19 (depends on who observation made)
rim: participation[typeCode=AUT].time

performer

Σ C

0..*

There are no (further) constraints on this element

Element id

Observation.performer

Short description

Who is responsible for the observation

Definition

Who was responsible for asserting the observed value as "true".

Requirements

May give a degree of confidence in the observation and also indicates where follow-up questions should be directed.

Comments

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ref-1: SHALL have a contained resource if a local reference is provided
reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))

Mappings

rim: n/a
rim: The target of a resource reference is a RIM entry point (Act, Role, or Entity)
workflow: Event.performer.actor
w5: FiveWs.actor
v2: OBX.15 / (Practitioner) OBX-16, PRT-5:PRT-4='RO' / (Device) OBX-18 , PRT-10:PRT-4='EQUIP' / (Organization) OBX-23, PRT-8:PRT-4='PO'
rim: participation[typeCode=PRF]

value[x]

S Σ C

0..1

Element id

Observation.value[x]

Short description

Actual result

Definition

The information determined as a result of making the observation, if the information has a simple value.

Requirements

An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

Comments

An observation may have; 1) a single value here, 2) both a value and a set of related or component values, or 3) only a set of related or component values. If a value is present, the datatype for this element should be determined by Observation.code. A CodeableConcept with just a text would be used instead of a string if the field was usually coded, or if the type associated with the Observation.code defines a coded value. For additional guidance, see the Notes section below.

Slicing

Unordered, Closed, by $this(Type)

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1, obs-7

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
sct-concept: < 441742003 |Evaluation finding|
v2: OBX.2, OBX.5, OBX.6
rim: value
sct-attr: 363714003 |Interprets|

valueCodeableConcept

S Σ C

0..1

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.value[x]:valueCodeableConcept

Short description

Indeterminate | No call | Present | Absent.

Definition

The presence or absence of the variant described in the components. If not searching for specific variations and merely reporting what's found, the profile's value should be set to 'Present'.

Requirements

An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

Comments

Data type

http://loinc.org/vs/LL1971-2 (required)

Binding

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1, obs-7

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
sct-concept: < 441742003 |Evaluation finding|
v2: OBX.2, OBX.5, OBX.6
rim: value
sct-attr: 363714003 |Interprets|

0..1

There are no (further) constraints on this element

Element id

Observation.value[x]:valueCodeableConcept.id

Short description

Unique id for inter-element referencing

Definition

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Data type

Mappings

rim: n/a

extension

0..*

There are no (further) constraints on this element

Element id

Observation.value[x]:valueCodeableConcept.extension

Short description

Additional content defined by implementations

Alternate names

extensions, user content

Definition

Comments

Data type

Slicing

Unordered, Open, by url(Value)

Extensions are always sliced by (at least) url

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

coding

0..*

There are no (further) constraints on this element

Element id

Observation.value[x]:valueCodeableConcept.coding

Short description

Code defined by a terminology system

Definition

A reference to a code defined by a terminology system.

Requirements

Allows for alternative encodings within a code system, and translations to other code systems.

Comments

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE subset one of the sets of component 1-3 or 4-6
rim: CV
orim: fhir:Coding rdfs:subClassOf dt:CDCoding
v2: C*E.1-8, C*E.10-22
rim: union(., ./translation)
orim: fhir:CodeableConcept.coding rdfs:subPropertyOf dt:CD.coding

0..1

There are no (further) constraints on this element

Element id

Observation.value[x]:valueCodeableConcept.coding.id

Short description

Unique id for inter-element referencing

Definition

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Data type

Mappings

rim: n/a

extension

0..*

There are no (further) constraints on this element

Element id

Observation.value[x]:valueCodeableConcept.coding.extension

Short description

Additional content defined by implementations

Alternate names

extensions, user content

Definition

Comments

Data type

Slicing

Unordered, Open, by url(Value)

Extensions are always sliced by (at least) url

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

system

S Σ

0..1

There are no (further) constraints on this element

Element id

Observation.value[x]:valueCodeableConcept.coding.system

Short description

Identity of the terminology system

Definition

The identification of the code system that defines the meaning of the symbol in the code.

Requirements

Need to be unambiguous about the source of the definition of the symbol.

Comments

The URI may be an OID (urn:oid:...) or a UUID (urn:uuid:...). OIDs and UUIDs SHALL be references to the HL7 OID registry. Otherwise, the URI should come from HL7's list of FHIR defined special URIs or it should reference to some definition that establishes the system clearly and unambiguously.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: C*E.3
rim: ./codeSystem
orim: fhir:Coding.system rdfs:subPropertyOf dt:CDCoding.codeSystem

version

0..1

There are no (further) constraints on this element

Element id

Observation.value[x]:valueCodeableConcept.coding.version

Short description

Version of the system - if relevant

Definition

The version of the code system which was used when choosing this code. Note that a well-maintained code system does not need the version reported, because the meaning of codes is consistent across versions. However this cannot consistently be assured, and when the meaning is not guaranteed to be consistent, the version SHOULD be exchanged.

Comments

Where the terminology does not clearly define what string should be used to identify code system versions, the recommendation is to use the date (expressed in FHIR date format) on which that version was officially published as the version date.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: C*E.7
rim: ./codeSystemVersion
orim: fhir:Coding.version rdfs:subPropertyOf dt:CDCoding.codeSystemVersion

code

S Σ

0..1

There are no (further) constraints on this element

Element id

Observation.value[x]:valueCodeableConcept.coding.code

Short description

Symbol in syntax defined by the system

Definition

A symbol in syntax defined by the system. The symbol may be a predefined code or an expression in a syntax defined by the coding system (e.g. post-coordination).

Requirements

Need to refer to a particular code in the system.

Comments

Note that FHIR strings SHALL NOT exceed 1MB in size

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: C*E.1
rim: ./code
orim: fhir:Coding.code rdfs:subPropertyOf dt:CDCoding.code

display

0..1

There are no (further) constraints on this element

Element id

Observation.value[x]:valueCodeableConcept.coding.display

Short description

Representation defined by the system

Definition

A representation of the meaning of the code in the system, following the rules of the system.

Requirements

Need to be able to carry a human-readable meaning of the code for readers that do not know the system.

Comments

Note that FHIR strings SHALL NOT exceed 1MB in size

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: C*E.2 - but note this is not well followed
rim: CV.displayName
orim: fhir:Coding.display rdfs:subPropertyOf dt:CDCoding.displayName

userSelected

0..1

There are no (further) constraints on this element

Element id

Observation.value[x]:valueCodeableConcept.coding.userSelected

Short description

If this coding was chosen directly by the user

Definition

Indicates that this coding was chosen by a user directly - e.g. off a pick list of available items (codes or displays).

Requirements

This has been identified as a clinical safety criterium - that this exact system/code pair was chosen explicitly, rather than inferred by the system based on some rules or language processing.

Comments

Amongst a set of alternatives, a directly chosen code is the most appropriate starting point for new translations. There is some ambiguity about what exactly 'directly chosen' implies, and trading partner agreement may be needed to clarify the use of this element and its consequences more completely.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: Sometimes implied by being first
rim: CD.codingRationale
orim: fhir:Coding.userSelected fhir:mapsTo dt:CDCoding.codingRationale. fhir:Coding.userSelected fhir:hasMap fhir:Coding.userSelected.map. fhir:Coding.userSelected.map a fhir:Map; fhir:target dt:CDCoding.codingRationale. fhir:Coding.userSelected\#true a [ fhir:source "true"; fhir:target dt:CDCoding.codingRationale\#O ]

text

0..1

There are no (further) constraints on this element

Element id

Observation.value[x]:valueCodeableConcept.text

Short description

Plain text representation of the concept

Definition

A human language representation of the concept as seen/selected/uttered by the user who entered the data and/or which represents the intended meaning of the user.

Requirements

Comments

Very often the text is the same as a displayName of one of the codings.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: C*E.9. But note many systems use C*E.2 for this
rim: ./originalText[mediaType/code="text/plain"]/data
orim: fhir:CodeableConcept.text rdfs:subPropertyOf dt:CD.originalText

dataAbsentReason

0..1

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.dataAbsentReason

Short description

Why the result is missing

Definition

Provides a reason why the expected value in the element Observation.value[x] is missing.

Requirements

For many results it is necessary to handle exceptional values in measurements.

Comments

Null or exceptional values can be represented two ways in FHIR Observations. One way is to simply include them in the value set and represent the exceptions in the value. For example, measurement values for a serology test could be "detected", "not detected", "inconclusive", or "specimen unsatisfactory".

The alternate way is to use the value element for actual observations and use the explicit dataAbsentReason element to record exceptional values. For example, the dataAbsentReason code "error" could be used when the measurement was not completed. Note that an observation may only be reported if there are values to report. For example differential cell counts values may be reported only when > 0. Because of these options, use-case agreements are required to interpret general observations for null or exceptional values.

Data type

Binding

Codes specifying why the result (Observation.value[x]) is missing.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1, obs-6

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
v2: N/A
rim: value.nullFlavor

interpretation

0..*

CodeableConceptBinding

Element id

Observation.interpretation

Short description

High, low, normal, etc.

Alternate names

Abnormal Flag

Definition

A categorical assessment of an observation value. For example, high, low, normal.

Requirements

For some results, particularly numeric results, an interpretation is necessary to fully understand the significance of a result.

Comments

Historically used for laboratory results (known as 'abnormal flag' ), its use extends to other use cases where coded interpretations are relevant. Often reported as one or more simple compact codes this element is often placed adjacent to the result value in reports and flow sheets to signal the meaning/normalcy status of the result.

Data type

Slicing

Unordered, Open, by $this(Type)

Binding

Codes identifying interpretations of observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
sct-concept: < 260245000 |Findings values|
v2: OBX-8
rim: interpretationCode
sct-attr: 363713009 |Has interpretation|
oBDS: 23.2

oBDS

0..1

CodeableConceptBinding

Element id

Observation.interpretation:oBDS

Short description

High, low, normal, etc.

Alternate names

Abnormal Flag

Definition

A categorical assessment of an observation value. For example, high, low, normal.

Requirements

For some results, particularly numeric results, an interpretation is necessary to fully understand the significance of a result.

Comments

Data type

MII_VS_Onko_Genetische_Variante_Auspraegung (required)

Binding

Codes identifying interpretations of observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
sct-concept: < 260245000 |Findings values|
v2: OBX-8
rim: interpretationCode
sct-attr: 363713009 |Has interpretation|

0..1

There are no (further) constraints on this element

Element id

Observation.interpretation:oBDS.id

Short description

Unique id for inter-element referencing

Definition

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Data type

Mappings

rim: n/a

extension

0..*

There are no (further) constraints on this element

Element id

Observation.interpretation:oBDS.extension

Short description

Additional content defined by implementations

Alternate names

extensions, user content

Definition

Comments

Data type

Slicing

Unordered, Open, by url(Value)

Extensions are always sliced by (at least) url

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

coding

0..*

Element id

Observation.interpretation:oBDS.coding

Short description

Genetische Variante Ausprägung

Definition

Genetische Variante Ausprägung gemäß 23.1 oBDS 2021

Requirements

Allows for alternative encodings within a code system, and translations to other code systems.

Comments

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE subset one of the sets of component 1-3 or 4-6
rim: CV
orim: fhir:Coding rdfs:subClassOf dt:CDCoding
v2: C*E.1-8, C*E.10-22
rim: union(., ./translation)
orim: fhir:CodeableConcept.coding rdfs:subPropertyOf dt:CD.coding

0..1

There are no (further) constraints on this element

Element id

Observation.interpretation:oBDS.coding.id

Short description

Unique id for inter-element referencing

Definition

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Data type

Mappings

rim: n/a

extension

0..*

There are no (further) constraints on this element

Element id

Observation.interpretation:oBDS.coding.extension

Short description

Additional content defined by implementations

Alternate names

extensions, user content

Definition

Comments

Data type

Slicing

Unordered, Open, by url(Value)

Extensions are always sliced by (at least) url

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

system

S Σ

0..1

There are no (further) constraints on this element

Element id

Observation.interpretation:oBDS.coding.system

Short description

Identity of the terminology system

Definition

The identification of the code system that defines the meaning of the symbol in the code.

Requirements

Need to be unambiguous about the source of the definition of the symbol.

Comments

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: C*E.3
rim: ./codeSystem
orim: fhir:Coding.system rdfs:subPropertyOf dt:CDCoding.codeSystem

version

0..1

There are no (further) constraints on this element

Element id

Observation.interpretation:oBDS.coding.version

Short description

Version of the system - if relevant

Definition

Comments

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: C*E.7
rim: ./codeSystemVersion
orim: fhir:Coding.version rdfs:subPropertyOf dt:CDCoding.codeSystemVersion

code

S Σ

0..1

There are no (further) constraints on this element

Element id

Observation.interpretation:oBDS.coding.code

Short description

Symbol in syntax defined by the system

Definition

A symbol in syntax defined by the system. The symbol may be a predefined code or an expression in a syntax defined by the coding system (e.g. post-coordination).

Requirements

Need to refer to a particular code in the system.

Comments

Note that FHIR strings SHALL NOT exceed 1MB in size

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: C*E.1
rim: ./code
orim: fhir:Coding.code rdfs:subPropertyOf dt:CDCoding.code

display

0..1

There are no (further) constraints on this element

Element id

Observation.interpretation:oBDS.coding.display

Short description

Representation defined by the system

Definition

A representation of the meaning of the code in the system, following the rules of the system.

Requirements

Need to be able to carry a human-readable meaning of the code for readers that do not know the system.

Comments

Note that FHIR strings SHALL NOT exceed 1MB in size

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: C*E.2 - but note this is not well followed
rim: CV.displayName
orim: fhir:Coding.display rdfs:subPropertyOf dt:CDCoding.displayName

userSelected

0..1

There are no (further) constraints on this element

Element id

Observation.interpretation:oBDS.coding.userSelected

Short description

If this coding was chosen directly by the user

Definition

Indicates that this coding was chosen by a user directly - e.g. off a pick list of available items (codes or displays).

Requirements

This has been identified as a clinical safety criterium - that this exact system/code pair was chosen explicitly, rather than inferred by the system based on some rules or language processing.

Comments

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: Sometimes implied by being first
rim: CD.codingRationale
orim: fhir:Coding.userSelected fhir:mapsTo dt:CDCoding.codingRationale. fhir:Coding.userSelected fhir:hasMap fhir:Coding.userSelected.map. fhir:Coding.userSelected.map a fhir:Map; fhir:target dt:CDCoding.codingRationale. fhir:Coding.userSelected\#true a [ fhir:source "true"; fhir:target dt:CDCoding.codingRationale\#O ]

text

0..1

There are no (further) constraints on this element

Element id

Observation.interpretation:oBDS.text

Short description

Plain text representation of the concept

Definition

A human language representation of the concept as seen/selected/uttered by the user who entered the data and/or which represents the intended meaning of the user.

Requirements

Comments

Very often the text is the same as a displayName of one of the codings.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: C*E.9. But note many systems use C*E.2 for this
rim: ./originalText[mediaType/code="text/plain"]/data
orim: fhir:CodeableConcept.text rdfs:subPropertyOf dt:CD.originalText

note

0..*

CodedAnnotation

Element id

Observation.note

Short description

Comments about the Observation that also contain a coded type

Definition

A text note which also contains information about who made the statement and when.

Requirements

Need to be able to provide free text additional information. Notes SHALL NOT contain information which can be captured in a structured way.

Comments

May include general statements about the observation, or statements about significant, unexpected or unreliable results values, or information about its source when relevant to its interpretation. The CodedAnnotation data type, while not allowing for or intending to make the content computable, does allow the author to indicate the type of note. This does not replace the use of interpretation, value, or component values. One important note is that Annotation is a FHIR data type, this is NOT about annotations in the genomic context.

Data type

CodedAnnotation

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: N/A
rim: Act
v2: NTE.3 (partner NTE to OBX, or sometimes another (child?) OBX)
rim: subjectOf.observationEvent[code="annotation"].value
oBDS: 23.1

0..1

There are no (further) constraints on this element

Element id

Observation.note.id

Short description

Unique id for inter-element referencing

Definition

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Data type

Mappings

rim: n/a

extension

0..*

There are no (further) constraints on this element

Element id

Observation.note.extension

Short description

Additional content defined by implementations

Alternate names

extensions, user content

Definition

Comments

Data type

Extension(CodeableConcept)

Slicing

Unordered, Open, by url(Value)

Extensions are always sliced by (at least) url

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

code

0..1

There are no (further) constraints on this element

Element id

Observation.note.extension:code

Short description

Annotation Code

Alternate names

extensions, user content

Definition

Codifies the content of an Annotation

Comments

Data type

Extension(CodeableConcept)

Extension URL

http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/annotation-code

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

author[x]

0..1

There are no (further) constraints on this element

Element id

Observation.note.author[x]

Short description

Individual responsible for the annotation

Definition

The individual responsible for making the annotation.

Comments

Organization is used when there's no need for specific attribution as to who made the comment.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: N/A
rim: Act.participant[typeCode=AUT].role

authorReference

Reference(Organization | Patient | Practitioner | RelatedPerson)

There are no (further) constraints on this element

Data type

Reference(Organization | Patient | Practitioner | RelatedPerson)

authorString

There are no (further) constraints on this element

Data type

time

0..1

There are no (further) constraints on this element

Element id

Observation.note.time

Short description

When the annotation was made

Definition

Indicates when this particular annotation was made.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: N/A
rim: Act.effectiveTime

text

S Σ

1..1

markdown

Element id

Observation.note.text

Short description

Genetische Variante Name

Definition

Genetische Variante Name gemäß 23.1 oBDS 2021

Comments

Systems are not required to have markdown support, so the text should be readable without markdown processing. The markdown syntax is GFM - see https://github.github.com/gfm/

Data type

markdown

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: N/A
rim: Act.text

bodySite

0..1

There are no (further) constraints on this element

Element id

Observation.bodySite

Short description

Observed body part

Definition

Indicates the site on the subject's body where the observation was made (i.e. the target site).

Comments

Only used if not implicit in code found in Observation.code. In many systems, this may be represented as a related observation instead of an inline component.

If the use case requires BodySite to be handled as a separate resource (e.g. to identify and track separately) then use the standard extension bodySite.

Data type

SNOMEDCTBodyStructures (example)

Binding

Codes describing anatomical locations. May include laterality.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
sct-concept: < 123037004 |Body structure|
v2: OBX-20
rim: targetSiteCode
sct-attr: 718497002 |Inherent location|

method

0..1

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.method

Short description

Sequencing | SNP array | PCR | Computational analysis | ...

Definition

Indicates the mechanism used to perform the observation.

Requirements

In some cases, method can impact results and is thus used for determining whether results can be compared or determining significance of results.

Comments

Only used if not implicit in code for Observation.code.

Data type

http://loinc.org/vs/LL4048-6 (extensible)

Binding

Methods for simple observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
v2: OBX-17
rim: methodCode

specimen

S C

0..1

Reference(Specimen)

There are no (further) constraints on this element

Element id

Observation.specimen

Short description

Specimen used for this observation

Definition

The specimen that was used when this observation was made.

Comments

Should only be used if not implicit in code found in Observation.code. Observations are not made on specimens themselves; they are made on a subject, but in many cases by the means of a specimen. Note that although specimens are often involved, they are not always tracked and reported explicitly. Also note that observation resources may be used in contexts that track the specimen explicitly (e.g. Diagnostic Report).

Data type

Reference(Specimen)

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ref-1: SHALL have a contained resource if a local reference is provided
reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))

Mappings

rim: n/a
rim: The target of a resource reference is a RIM entry point (Act, Role, or Entity)
sct-concept: < 123038009 |Specimen|
v2: SPM segment
rim: participation[typeCode=SPC].specimen
sct-attr: 704319004 |Inherent in|

device

S C

0..1

Reference(Device | DeviceMetric)

There are no (further) constraints on this element

Element id

Observation.device

Short description

(Measurement) Device

Definition

The device used to generate the observation data.

Comments

Note that this is not meant to represent a device involved in the transmission of the result, e.g., a gateway. Such devices may be documented using the Provenance resource where relevant.

Data type

Reference(Device | DeviceMetric)

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ref-1: SHALL have a contained resource if a local reference is provided
reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))

Mappings

rim: n/a
rim: The target of a resource reference is a RIM entry point (Act, Role, or Entity)
sct-concept: < 49062001 |Device|
v2: OBX-17 / PRT -10
rim: participation[typeCode=DEV]
sct-attr: 424226004 |Using device|

referenceRange

0..*

There are no (further) constraints on this element

Element id

Observation.referenceRange

Short description

Provides guide for interpretation

Definition

Guidance on how to interpret the value by comparison to a normal or recommended range. Multiple reference ranges are interpreted as an "OR". In other words, to represent two distinct target populations, two referenceRange elements would be used.

Requirements

Knowing what values are considered "normal" can help evaluate the significance of a particular result. Need to be able to provide multiple reference ranges for different contexts.

Comments

Most observations only have one generic reference range. Systems MAY choose to restrict to only supplying the relevant reference range based on knowledge about the patient (e.g., specific to the patient's age, gender, weight and other factors), but this might not be possible or appropriate. Whenever more than one reference range is supplied, the differences between them SHOULD be provided in the reference range and/or age properties.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
obs-3: Must have at least a low or a high or text
low.exists() or high.exists() or text.exists()

Mappings

rim: n/a
v2: OBX.7
rim: outboundRelationship[typeCode=REFV]/target[classCode=OBS, moodCode=EVN]

0..1

There are no (further) constraints on this element

Element id

Observation.referenceRange.id

Short description

Unique id for inter-element referencing

Definition

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Data type

Mappings

rim: n/a

extension

0..*

There are no (further) constraints on this element

Element id

Observation.referenceRange.extension

Short description

Additional content defined by implementations

Alternate names

extensions, user content

Definition

Comments

Data type

Slicing

Unordered, Open, by url(Value)

Extensions are always sliced by (at least) url

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

modifierExtension

Σ ?! C

0..*

There are no (further) constraints on this element

Element id

Observation.referenceRange.modifierExtension

Short description

Extensions that cannot be ignored even if unrecognized

Alternate names

extensions, user content, modifiers

Definition

May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

Requirements

Comments

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

low

0..1

There are no (further) constraints on this element

Element id

Observation.referenceRange.low

Short description

Low Range, if relevant

Definition

The value of the low bound of the reference range. The low bound of the reference range endpoint is inclusive of the value (e.g. reference range is >=5 - <=9). If the low bound is omitted, it is assumed to be meaningless (e.g. reference range is <=2.3).

Comments

The context of use may frequently define what kind of quantity this is and therefore what kind of units can be used. The context of use may also restrict the values for the comparator.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1, obs-3

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
qty-3: If a code for the unit is present, the system SHALL also be present
code.empty() or system.exists()
sqty-1: The comparator is not used on a SimpleQuantity
comparator.empty()

Mappings

rim: n/a
v2: SN (see also Range) or CQ
rim: PQ, IVL<PQ>, MO, CO, depending on the values
v2: OBX-7
rim: value:IVL_PQ.low

high

0..1

There are no (further) constraints on this element

Element id

Observation.referenceRange.high

Short description

High Range, if relevant

Definition

The value of the high bound of the reference range. The high bound of the reference range endpoint is inclusive of the value (e.g. reference range is >=5 - <=9). If the high bound is omitted, it is assumed to be meaningless (e.g. reference range is >= 2.3).

Comments

The context of use may frequently define what kind of quantity this is and therefore what kind of units can be used. The context of use may also restrict the values for the comparator.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1, obs-3

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
qty-3: If a code for the unit is present, the system SHALL also be present
code.empty() or system.exists()
sqty-1: The comparator is not used on a SimpleQuantity
comparator.empty()

Mappings

rim: n/a
v2: SN (see also Range) or CQ
rim: PQ, IVL<PQ>, MO, CO, depending on the values
v2: OBX-7
rim: value:IVL_PQ.high

type

0..1

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.referenceRange.type

Short description

Reference range qualifier

Definition

Codes to indicate the what part of the targeted reference population it applies to. For example, the normal or therapeutic range.

Requirements

Need to be able to say what kind of reference range this is - normal, recommended, therapeutic, etc., - for proper interpretation.

Comments

This SHOULD be populated if there is more than one range. If this element is not present then the normal range is assumed.

Data type

ObservationReferenceRangeMeaningCodes (preferred)

Binding

Code for the meaning of a reference range.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
sct-concept: < 260245000 |Findings values| OR < 365860008 |General clinical state finding| OR < 250171008 |Clinical history or observation findings| OR < 415229000 |Racial group| OR < 365400002 |Finding of puberty stage| OR < 443938003 |Procedure carried out on subject|
v2: OBX-10
rim: interpretationCode

appliesTo

0..*

There are no (further) constraints on this element

Element id

Observation.referenceRange.appliesTo

Short description

Reference range population

Definition

Codes to indicate the target population this reference range applies to. For example, a reference range may be based on the normal population or a particular sex or race. Multiple appliesTo are interpreted as an "AND" of the target populations. For example, to represent a target population of African American females, both a code of female and a code for African American would be used.

Requirements

Need to be able to identify the target population for proper interpretation.

Comments

This SHOULD be populated if there is more than one range. If this element is not present then the normal population is assumed.

Data type

ObservationReferenceRangeAppliesToCodes (example)

Binding

Codes identifying the population the reference range applies to.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
sct-concept: < 260245000 |Findings values| OR < 365860008 |General clinical state finding| OR < 250171008 |Clinical history or observation findings| OR < 415229000 |Racial group| OR < 365400002 |Finding of puberty stage| OR < 443938003 |Procedure carried out on subject|
v2: OBX-10
rim: interpretationCode

age

0..1

There are no (further) constraints on this element

Element id

Observation.referenceRange.age

Short description

Applicable age range, if relevant

Definition

The age at which this reference range is applicable. This is a neonatal age (e.g. number of weeks at term) if the meaning says so.

Requirements

Some analytes vary greatly over age.

Comments

The stated low and high value are assumed to have arbitrarily high precision when it comes to determining which values are in the range. I.e. 1.99 is not in the range 2 -> 3.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
rng-2: If present, low SHALL have a lower value than high
low.empty() or high.empty() or (low <= high)

Mappings

rim: n/a
v2: NR and also possibly SN (but see also quantity)
rim: IVL<QTY[not(type="TS")]> [lowClosed="true" and highClosed="true"]or URG<QTY[not(type="TS")]>
rim: outboundRelationship[typeCode=PRCN].targetObservationCriterion[code="age"].value

text

0..1

There are no (further) constraints on this element

Element id

Observation.referenceRange.text

Short description

Text based reference range in an observation

Definition

Text based reference range in an observation which may be used when a quantitative range is not appropriate for an observation. An example would be a reference value of "Negative" or a list or table of "normals".

Comments

Note that FHIR strings SHALL NOT exceed 1MB in size

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: OBX-7
rim: value:ST

hasMember

Σ C

0..*

Reference(MolecularSequence | Observation | QuestionnaireResponse)

There are no (further) constraints on this element

Element id

Observation.hasMember

Short description

Related resource that belongs to the Observation group

Definition

This observation is a group observation (e.g. a battery, a panel of tests, a set of vital sign measurements) that includes the target as a member of the group.

Comments

When using this element, an observation will typically have either a value or a set of related resources, although both may be present in some cases. For a discussion on the ways Observations can assembled in groups together, see Notes below. Note that a system may calculate results from QuestionnaireResponse into a final score and represent the score as an Observation.

Data type

Reference(MolecularSequence | Observation | QuestionnaireResponse)

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ref-1: SHALL have a contained resource if a local reference is provided
reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))

Mappings

rim: n/a
rim: The target of a resource reference is a RIM entry point (Act, Role, or Entity)
v2: Relationships established by OBX-4 usage
rim: outBoundRelationship

derivedFrom

Σ C

0..*

There are no (further) constraints on this element

Element id

Observation.derivedFrom

Short description

Related measurements the observation is made from

Definition

The target resource that represents a measurement from which this observation value is derived. For example, a calculated anion gap or a fetal measurement based on an ultrasound image.

Comments

All the reference choices that are listed in this element can represent clinical observations and other measurements that may be the source for a derived value. The most common reference will be another Observation. For a discussion on the ways Observations can assembled in groups together, see Notes below.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ref-1: SHALL have a contained resource if a local reference is provided
reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))

Mappings

rim: n/a
rim: The target of a resource reference is a RIM entry point (Act, Role, or Entity)
v2: Relationships established by OBX-4 usage
rim: .targetObservation

component

0..*

There are no (further) constraints on this element

Element id

Observation.component

Short description

Component results

Definition

Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations.

Requirements

Component observations share the same attributes in the Observation resource as the primary observation and are always treated a part of a single observation (they are not separable). However, the reference range for the primary observation value is not inherited by the component values and is required when appropriate for each component observation.

Comments

For a discussion on the ways Observations can be assembled in groups together see Notes below.

Data type

Slicing

Unordered, Open, by code(Pattern)

Slice based on the component.code pattern

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: containment by OBX-4?
rim: outBoundRelationship[typeCode=COMP]

(All Slices)

The requirements in this element apply to all slices

0..1

There are no (further) constraints on this element

Element id

Observation.component.id

Short description

Unique id for inter-element referencing

Definition

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Data type

Mappings

rim: n/a

extension

0..*

There are no (further) constraints on this element

Element id

Observation.component.extension

Short description

Additional content defined by implementations

Alternate names

extensions, user content

Definition

Comments

Data type

Slicing

Unordered, Open, by url(Value)

Extensions are always sliced by (at least) url

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

modifierExtension

Σ ?! C

0..*

There are no (further) constraints on this element

Element id

Observation.component.modifierExtension

Short description

Extensions that cannot be ignored even if unrecognized

Alternate names

extensions, user content, modifiers

Definition

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

Requirements

Comments

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

code

1..1

There are no (further) constraints on this element

Element id

Observation.component.code

Short description

Type of component observation (code / type)

Definition

Describes what was observed. Sometimes this is called the observation "code".

Requirements

Knowing what kind of observation is being made is essential to understanding the observation.

Comments

All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

Data type

Binding

Codes identifying names of simple observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
w5: FiveWs.what[x]
sct-concept: < 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
v2: OBX-3
rim: code

value[x]

0..1

There are no (further) constraints on this element

Element id

Observation.component.value[x]

Short description

Actual component result

Definition

The information determined as a result of making the observation, if the information has a simple value.

Requirements

An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

Comments

Used when observation has a set of component observations. An observation may have both a value (e.g. an Apgar score) and component observations (the observations from which the Apgar score was derived). If a value is present, the datatype for this element should be determined by Observation.code. A CodeableConcept with just a text would be used instead of a string if the field was usually coded, or if the type associated with the Observation.code defines a coded value. For additional guidance, see the Notes section below.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
sct-concept: 363714003 |Interprets| < 441742003 |Evaluation finding|
v2: OBX.2, OBX.5, OBX.6
rim: value
sct-attr: 363714003 |Interprets|

valueBoolean

There are no (further) constraints on this element

Data type

valueCodeableConcept

There are no (further) constraints on this element

Data type

valueDateTime

There are no (further) constraints on this element

Data type

valueInteger

integer

There are no (further) constraints on this element

Data type

integer

valuePeriod

There are no (further) constraints on this element

Data type

valueQuantity

There are no (further) constraints on this element

Data type

valueRange

There are no (further) constraints on this element

Data type

valueRatio

Ratio

There are no (further) constraints on this element

Data type

Ratio

valueSampledData

SampledData

There are no (further) constraints on this element

Data type

SampledData

valueString

There are no (further) constraints on this element

Data type

valueTime

time

There are no (further) constraints on this element

Data type

time

dataAbsentReason

0..1

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component.dataAbsentReason

Short description

Why the component result is missing

Definition

Provides a reason why the expected value in the element Observation.component.value[x] is missing.

Requirements

For many results it is necessary to handle exceptional values in measurements.

Comments

"Null" or exceptional values can be represented two ways in FHIR Observations. One way is to simply include them in the value set and represent the exceptions in the value. For example, measurement values for a serology test could be "detected", "not detected", "inconclusive", or "test not done".

Data type

Binding

Codes specifying why the result (Observation.value[x]) is missing.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1, obs-6

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
v2: N/A
rim: value.nullFlavor

interpretation

0..*

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component.interpretation

Short description

High, low, normal, etc.

Alternate names

Abnormal Flag

Definition

A categorical assessment of an observation value. For example, high, low, normal.

Requirements

For some results, particularly numeric results, an interpretation is necessary to fully understand the significance of a result.

Comments

Data type

Binding

Codes identifying interpretations of observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
sct-concept: < 260245000 |Findings values|
v2: OBX-8
rim: interpretationCode
sct-attr: 363713009 |Has interpretation|

referenceRange

0..*

There are no (further) constraints on this element

Element id

Observation.component.referenceRange

Short description

Provides guide for interpretation of component result

Definition

Guidance on how to interpret the value by comparison to a normal or recommended range.

Requirements

Knowing what values are considered "normal" can help evaluate the significance of a particular result. Need to be able to provide multiple reference ranges for different contexts.

Comments

Mappings

v2: OBX.7
rim: outboundRelationship[typeCode=REFV]/target[classCode=OBS, moodCode=EVN]

conclusion-string

S Σ

0..1

There are no (further) constraints on this element

Element id

Observation.component:conclusion-string

Short description

Clinical Conclusion

Definition

Concise and clinically contextualized summary conclusion (interpretation/impression) of the observation

Requirements

Need to be able to provide a conclusion that is not lost among the basic result data.

Comments

An example would be the interpretative information, typically canned, about a variant identified in the patient.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: containment by OBX-4?
rim: outBoundRelationship[typeCode=COMP]

0..1

There are no (further) constraints on this element

Element id

Observation.component:conclusion-string.id

Short description

Unique id for inter-element referencing

Definition

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Data type

Mappings

rim: n/a

extension

0..*

There are no (further) constraints on this element

Element id

Observation.component:conclusion-string.extension

Short description

Additional content defined by implementations

Alternate names

extensions, user content

Definition

Comments

Data type

Slicing

Unordered, Open, by url(Value)

Extensions are always sliced by (at least) url

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

modifierExtension

Σ ?! C

0..*

There are no (further) constraints on this element

Element id

Observation.component:conclusion-string.modifierExtension

Short description

Extensions that cannot be ignored even if unrecognized

Alternate names

extensions, user content, modifiers

Definition

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

Requirements

Comments

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

code

1..1

CodeableConceptPattern

There are no (further) constraints on this element

Element id

Observation.component:conclusion-string.code

Short description

conclusion-string

Definition

Describes what was observed. Sometimes this is called the observation "code".

Requirements

Knowing what kind of observation is being made is essential to understanding the observation.

Comments

All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

Data type

Binding

Codes identifying names of simple observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Pattern

{
  "coding": [
    {
      "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
      "code": "conclusion-string"
    }
  ]
}

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
w5: FiveWs.what[x]
sct-concept: < 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
v2: OBX-3
rim: code

value[x]

0..1

There are no (further) constraints on this element

Element id

Observation.component:conclusion-string.value[x]

Short description

Summary conclusion (interpretation/impression)

Definition

The information determined as a result of making the observation, if the information has a simple value.

Requirements

An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

Comments

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
sct-concept: 363714003 |Interprets| < 441742003 |Evaluation finding|
v2: OBX.2, OBX.5, OBX.6
rim: value
sct-attr: 363714003 |Interprets|

valueString

There are no (further) constraints on this element

Data type

dataAbsentReason

0..1

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:conclusion-string.dataAbsentReason

Short description

Why the component result is missing

Definition

Provides a reason why the expected value in the element Observation.component.value[x] is missing.

Requirements

For many results it is necessary to handle exceptional values in measurements.

Comments

Data type

Binding

Codes specifying why the result (Observation.value[x]) is missing.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1, obs-6

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
v2: N/A
rim: value.nullFlavor

interpretation

0..*

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:conclusion-string.interpretation

Short description

High, low, normal, etc.

Alternate names

Abnormal Flag

Definition

A categorical assessment of an observation value. For example, high, low, normal.

Requirements

For some results, particularly numeric results, an interpretation is necessary to fully understand the significance of a result.

Comments

Data type

Binding

Codes identifying interpretations of observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
sct-concept: < 260245000 |Findings values|
v2: OBX-8
rim: interpretationCode
sct-attr: 363713009 |Has interpretation|

referenceRange

0..*

There are no (further) constraints on this element

Element id

Observation.component:conclusion-string.referenceRange

Short description

Provides guide for interpretation of component result

Definition

Guidance on how to interpret the value by comparison to a normal or recommended range.

Requirements

Knowing what values are considered "normal" can help evaluate the significance of a particular result. Need to be able to provide multiple reference ranges for different contexts.

Comments

Mappings

v2: OBX.7
rim: outboundRelationship[typeCode=REFV]/target[classCode=OBS, moodCode=EVN]

gene-studied

S Σ

0..*

There are no (further) constraints on this element

Element id

Observation.component:gene-studied

Short description

Gene Studied

Definition

The gene(s) on which the variant is located.

Requirements

Comments

For a discussion on the ways Observations can be assembled in groups together see Notes below.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: containment by OBX-4?
rim: outBoundRelationship[typeCode=COMP]
MII-KDS: mide-dataelement-1400

0..1

There are no (further) constraints on this element

Element id

Observation.component:gene-studied.id

Short description

Unique id for inter-element referencing

Definition

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Data type

Mappings

rim: n/a

extension

0..*

There are no (further) constraints on this element

Element id

Observation.component:gene-studied.extension

Short description

Additional content defined by implementations

Alternate names

extensions, user content

Definition

Comments

Data type

Slicing

Unordered, Open, by url(Value)

Extensions are always sliced by (at least) url

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

modifierExtension

Σ ?! C

0..*

There are no (further) constraints on this element

Element id

Observation.component:gene-studied.modifierExtension

Short description

Extensions that cannot be ignored even if unrecognized

Alternate names

extensions, user content, modifiers

Definition

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

Requirements

Comments

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

code

1..1

CodeableConceptPattern

There are no (further) constraints on this element

Element id

Observation.component:gene-studied.code

Short description

48018-6

Definition

Describes what was observed. Sometimes this is called the observation "code".

Requirements

Knowing what kind of observation is being made is essential to understanding the observation.

Comments

All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

Data type

Binding

Codes identifying names of simple observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Pattern

{
  "coding": [
    {
      "system": "http://loinc.org",
      "code": "48018-6"
    }
  ]
}

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
w5: FiveWs.what[x]
sct-concept: < 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
v2: OBX-3
rim: code

value[x]

1..1

Binding

There are no (further) constraints on this element

Element id

Observation.component:gene-studied.value[x]

Short description

The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used.

Definition

The information determined as a result of making the observation, if the information has a simple value.

Requirements

An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

Comments

Binding

HGNCVS (extensible)

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
sct-concept: 363714003 |Interprets| < 441742003 |Evaluation finding|
v2: OBX.2, OBX.5, OBX.6
rim: value
sct-attr: 363714003 |Interprets|

valueCodeableConcept

There are no (further) constraints on this element

Data type

dataAbsentReason

0..1

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:gene-studied.dataAbsentReason

Short description

Why the component result is missing

Definition

Provides a reason why the expected value in the element Observation.component.value[x] is missing.

Requirements

For many results it is necessary to handle exceptional values in measurements.

Comments

Data type

Binding

Codes specifying why the result (Observation.value[x]) is missing.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1, obs-6

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
v2: N/A
rim: value.nullFlavor

interpretation

0..*

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:gene-studied.interpretation

Short description

High, low, normal, etc.

Alternate names

Abnormal Flag

Definition

A categorical assessment of an observation value. For example, high, low, normal.

Requirements

For some results, particularly numeric results, an interpretation is necessary to fully understand the significance of a result.

Comments

Data type

Binding

Codes identifying interpretations of observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
sct-concept: < 260245000 |Findings values|
v2: OBX-8
rim: interpretationCode
sct-attr: 363713009 |Has interpretation|

referenceRange

0..*

There are no (further) constraints on this element

Element id

Observation.component:gene-studied.referenceRange

Short description

Provides guide for interpretation of component result

Definition

Guidance on how to interpret the value by comparison to a normal or recommended range.

Requirements

Knowing what values are considered "normal" can help evaluate the significance of a particular result. Need to be able to provide multiple reference ranges for different contexts.

Comments

Mappings

v2: OBX.7
rim: outboundRelationship[typeCode=REFV]/target[classCode=OBS, moodCode=EVN]

cytogenetic-location

S Σ

0..*

There are no (further) constraints on this element

Element id

Observation.component:cytogenetic-location

Short description

Cytogenetic (Chromosome) Location

Definition

The relevant chromosomal region. The combination of numbers and letters provide a genetic 'address'.

Requirements

Comments

For a discussion on the ways Observations can be assembled in groups together see Notes below.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: containment by OBX-4?
rim: outBoundRelationship[typeCode=COMP]

0..1

There are no (further) constraints on this element

Element id

Observation.component:cytogenetic-location.id

Short description

Unique id for inter-element referencing

Definition

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Data type

Mappings

rim: n/a

extension

0..*

There are no (further) constraints on this element

Element id

Observation.component:cytogenetic-location.extension

Short description

Additional content defined by implementations

Alternate names

extensions, user content

Definition

Comments

Data type

Slicing

Unordered, Open, by url(Value)

Extensions are always sliced by (at least) url

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

modifierExtension

Σ ?! C

0..*

There are no (further) constraints on this element

Element id

Observation.component:cytogenetic-location.modifierExtension

Short description

Extensions that cannot be ignored even if unrecognized

Alternate names

extensions, user content, modifiers

Definition

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

Requirements

Comments

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

code

1..1

CodeableConceptPattern

There are no (further) constraints on this element

Element id

Observation.component:cytogenetic-location.code

Short description

48001-2

Definition

Describes what was observed. Sometimes this is called the observation "code".

Requirements

Knowing what kind of observation is being made is essential to understanding the observation.

Comments

All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

Data type

Binding

Codes identifying names of simple observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Pattern

{
  "coding": [
    {
      "system": "http://loinc.org",
      "code": "48001-2"
    }
  ]
}

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
w5: FiveWs.what[x]
sct-concept: < 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
v2: OBX-3
rim: code

value[x]

1..1

There are no (further) constraints on this element

Element id

Observation.component:cytogenetic-location.value[x]

Short description

Example: 1q21.1

Definition

The information determined as a result of making the observation, if the information has a simple value.

Requirements

An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

Comments

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
sct-concept: 363714003 |Interprets| < 441742003 |Evaluation finding|
v2: OBX.2, OBX.5, OBX.6
rim: value
sct-attr: 363714003 |Interprets|

valueCodeableConcept

There are no (further) constraints on this element

Data type

dataAbsentReason

0..1

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:cytogenetic-location.dataAbsentReason

Short description

Why the component result is missing

Definition

Provides a reason why the expected value in the element Observation.component.value[x] is missing.

Requirements

For many results it is necessary to handle exceptional values in measurements.

Comments

Data type

Binding

Codes specifying why the result (Observation.value[x]) is missing.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1, obs-6

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
v2: N/A
rim: value.nullFlavor

interpretation

0..*

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:cytogenetic-location.interpretation

Short description

High, low, normal, etc.

Alternate names

Abnormal Flag

Definition

A categorical assessment of an observation value. For example, high, low, normal.

Requirements

For some results, particularly numeric results, an interpretation is necessary to fully understand the significance of a result.

Comments

Data type

Binding

Codes identifying interpretations of observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
sct-concept: < 260245000 |Findings values|
v2: OBX-8
rim: interpretationCode
sct-attr: 363713009 |Has interpretation|

referenceRange

0..*

There are no (further) constraints on this element

Element id

Observation.component:cytogenetic-location.referenceRange

Short description

Provides guide for interpretation of component result

Definition

Guidance on how to interpret the value by comparison to a normal or recommended range.

Requirements

Knowing what values are considered "normal" can help evaluate the significance of a particular result. Need to be able to provide multiple reference ranges for different contexts.

Comments

Mappings

v2: OBX.7
rim: outboundRelationship[typeCode=REFV]/target[classCode=OBS, moodCode=EVN]

reference-sequence-assembly

S Σ

0..*

There are no (further) constraints on this element

Element id

Observation.component:reference-sequence-assembly

Short description

Human Reference Sequence Assembly

Definition

The reference genome/assembly used in this analysis.

Requirements

Comments

For a discussion on the ways Observations can be assembled in groups together see Notes below.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: containment by OBX-4?
rim: outBoundRelationship[typeCode=COMP]

0..1

There are no (further) constraints on this element

Element id

Observation.component:reference-sequence-assembly.id

Short description

Unique id for inter-element referencing

Definition

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Data type

Mappings

rim: n/a

extension

0..*

There are no (further) constraints on this element

Element id

Observation.component:reference-sequence-assembly.extension

Short description

Additional content defined by implementations

Alternate names

extensions, user content

Definition

Comments

Data type

Slicing

Unordered, Open, by url(Value)

Extensions are always sliced by (at least) url

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

modifierExtension

Σ ?! C

0..*

There are no (further) constraints on this element

Element id

Observation.component:reference-sequence-assembly.modifierExtension

Short description

Extensions that cannot be ignored even if unrecognized

Alternate names

extensions, user content, modifiers

Definition

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

Requirements

Comments

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

code

1..1

CodeableConceptPattern

There are no (further) constraints on this element

Element id

Observation.component:reference-sequence-assembly.code

Short description

62374-4

Definition

Describes what was observed. Sometimes this is called the observation "code".

Requirements

Knowing what kind of observation is being made is essential to understanding the observation.

Comments

All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

Data type

Binding

Codes identifying names of simple observations.

http://loinc.org/vs/LL1040-6 (extensible)

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Pattern

{
  "coding": [
    {
      "system": "http://loinc.org",
      "code": "62374-4"
    }
  ]
}

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
w5: FiveWs.what[x]
sct-concept: < 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
v2: OBX-3
rim: code

value[x]

1..1

Binding

There are no (further) constraints on this element

Element id

Observation.component:reference-sequence-assembly.value[x]

Short description

GRCh37 | GRCh38 | ...

Definition

The information determined as a result of making the observation, if the information has a simple value.

Requirements

An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

Comments

Binding

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
sct-concept: 363714003 |Interprets| < 441742003 |Evaluation finding|
v2: OBX.2, OBX.5, OBX.6
rim: value
sct-attr: 363714003 |Interprets|

valueCodeableConcept

There are no (further) constraints on this element

Data type

dataAbsentReason

0..1

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:reference-sequence-assembly.dataAbsentReason

Short description

Why the component result is missing

Definition

Provides a reason why the expected value in the element Observation.component.value[x] is missing.

Requirements

For many results it is necessary to handle exceptional values in measurements.

Comments

Data type

Binding

Codes specifying why the result (Observation.value[x]) is missing.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1, obs-6

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
v2: N/A
rim: value.nullFlavor

interpretation

0..*

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:reference-sequence-assembly.interpretation

Short description

High, low, normal, etc.

Alternate names

Abnormal Flag

Definition

A categorical assessment of an observation value. For example, high, low, normal.

Requirements

For some results, particularly numeric results, an interpretation is necessary to fully understand the significance of a result.

Comments

Data type

Binding

Codes identifying interpretations of observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
sct-concept: < 260245000 |Findings values|
v2: OBX-8
rim: interpretationCode
sct-attr: 363713009 |Has interpretation|

referenceRange

0..*

There are no (further) constraints on this element

Element id

Observation.component:reference-sequence-assembly.referenceRange

Short description

Provides guide for interpretation of component result

Definition

Guidance on how to interpret the value by comparison to a normal or recommended range.

Requirements

Knowing what values are considered "normal" can help evaluate the significance of a particular result. Need to be able to provide multiple reference ranges for different contexts.

Comments

Mappings

v2: OBX.7
rim: outboundRelationship[typeCode=REFV]/target[classCode=OBS, moodCode=EVN]

coding-hgvs

S Σ

0..1

There are no (further) constraints on this element

Element id

Observation.component:coding-hgvs

Short description

Coding (cDNA) Change - cHGVS

Definition

Description of the coding (cDNA) sequence change using a valid HGVS-formatted string.

Requirements

Comments

For a discussion on the ways Observations can be assembled in groups together see Notes below.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: containment by OBX-4?
rim: outBoundRelationship[typeCode=COMP]

0..1

There are no (further) constraints on this element

Element id

Observation.component:coding-hgvs.id

Short description

Unique id for inter-element referencing

Definition

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Data type

Mappings

rim: n/a

extension

0..*

There are no (further) constraints on this element

Element id

Observation.component:coding-hgvs.extension

Short description

Additional content defined by implementations

Alternate names

extensions, user content

Definition

Comments

Data type

Slicing

Unordered, Open, by url(Value)

Extensions are always sliced by (at least) url

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

modifierExtension

Σ ?! C

0..*

There are no (further) constraints on this element

Element id

Observation.component:coding-hgvs.modifierExtension

Short description

Extensions that cannot be ignored even if unrecognized

Alternate names

extensions, user content, modifiers

Definition

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

Requirements

Comments

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

code

1..1

CodeableConceptPattern

There are no (further) constraints on this element

Element id

Observation.component:coding-hgvs.code

Short description

48004-6

Definition

Describes what was observed. Sometimes this is called the observation "code".

Requirements

Knowing what kind of observation is being made is essential to understanding the observation.

Comments

All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

Data type

Binding

Codes identifying names of simple observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Pattern

{
  "coding": [
    {
      "system": "http://loinc.org",
      "code": "48004-6"
    }
  ]
}

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
w5: FiveWs.what[x]
sct-concept: < 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
v2: OBX-3
rim: code

value[x]

1..1

Binding

There are no (further) constraints on this element

Element id

Observation.component:coding-hgvs.value[x]

Short description

A valid HGVS-formatted 'c.' string, e.g. NM_005228.5:c.2369C>T.

Definition

The information determined as a result of making the observation, if the information has a simple value.

Requirements

An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

Comments

Binding

HGVSVS (required)

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
sct-concept: 363714003 |Interprets| < 441742003 |Evaluation finding|
v2: OBX.2, OBX.5, OBX.6
rim: value
sct-attr: 363714003 |Interprets|

valueCodeableConcept

There are no (further) constraints on this element

Data type

dataAbsentReason

0..1

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:coding-hgvs.dataAbsentReason

Short description

Why the component result is missing

Definition

Provides a reason why the expected value in the element Observation.component.value[x] is missing.

Requirements

For many results it is necessary to handle exceptional values in measurements.

Comments

Data type

Binding

Codes specifying why the result (Observation.value[x]) is missing.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1, obs-6

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
v2: N/A
rim: value.nullFlavor

interpretation

0..*

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:coding-hgvs.interpretation

Short description

High, low, normal, etc.

Alternate names

Abnormal Flag

Definition

A categorical assessment of an observation value. For example, high, low, normal.

Requirements

For some results, particularly numeric results, an interpretation is necessary to fully understand the significance of a result.

Comments

Data type

Binding

Codes identifying interpretations of observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
sct-concept: < 260245000 |Findings values|
v2: OBX-8
rim: interpretationCode
sct-attr: 363713009 |Has interpretation|

referenceRange

0..*

There are no (further) constraints on this element

Element id

Observation.component:coding-hgvs.referenceRange

Short description

Provides guide for interpretation of component result

Definition

Guidance on how to interpret the value by comparison to a normal or recommended range.

Requirements

Knowing what values are considered "normal" can help evaluate the significance of a particular result. Need to be able to provide multiple reference ranges for different contexts.

Comments

Mappings

v2: OBX.7
rim: outboundRelationship[typeCode=REFV]/target[classCode=OBS, moodCode=EVN]

genomic-hgvs

S Σ

0..1

There are no (further) constraints on this element

Element id

Observation.component:genomic-hgvs

Short description

Genomic (gDNA) Change - gHGVS

Definition

Description of the genomic (gDNA) sequence change using a valid HGVS-formatted string.

Requirements

Comments

For a discussion on the ways Observations can be assembled in groups together see Notes below.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: containment by OBX-4?
rim: outBoundRelationship[typeCode=COMP]

0..1

There are no (further) constraints on this element

Element id

Observation.component:genomic-hgvs.id

Short description

Unique id for inter-element referencing

Definition

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Data type

Mappings

rim: n/a

extension

0..*

There are no (further) constraints on this element

Element id

Observation.component:genomic-hgvs.extension

Short description

Additional content defined by implementations

Alternate names

extensions, user content

Definition

Comments

Data type

Slicing

Unordered, Open, by url(Value)

Extensions are always sliced by (at least) url

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

modifierExtension

Σ ?! C

0..*

There are no (further) constraints on this element

Element id

Observation.component:genomic-hgvs.modifierExtension

Short description

Extensions that cannot be ignored even if unrecognized

Alternate names

extensions, user content, modifiers

Definition

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

Requirements

Comments

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

code

1..1

CodeableConceptPattern

There are no (further) constraints on this element

Element id

Observation.component:genomic-hgvs.code

Short description

81290-9

Definition

Describes what was observed. Sometimes this is called the observation "code".

Requirements

Knowing what kind of observation is being made is essential to understanding the observation.

Comments

All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

Data type

Binding

Codes identifying names of simple observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Pattern

{
  "coding": [
    {
      "system": "http://loinc.org",
      "code": "81290-9"
    }
  ]
}

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
w5: FiveWs.what[x]
sct-concept: < 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
v2: OBX-3
rim: code

value[x]

1..1

Binding

There are no (further) constraints on this element

Element id

Observation.component:genomic-hgvs.value[x]

Short description

A valid HGVS-formatted 'g.' string, e.g. NC_000016.9:g.2124200_2138612dup

Definition

The information determined as a result of making the observation, if the information has a simple value.

Requirements

An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

Comments

Binding

HGVSVS (required)

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
sct-concept: 363714003 |Interprets| < 441742003 |Evaluation finding|
v2: OBX.2, OBX.5, OBX.6
rim: value
sct-attr: 363714003 |Interprets|

valueCodeableConcept

There are no (further) constraints on this element

Data type

dataAbsentReason

0..1

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:genomic-hgvs.dataAbsentReason

Short description

Why the component result is missing

Definition

Provides a reason why the expected value in the element Observation.component.value[x] is missing.

Requirements

For many results it is necessary to handle exceptional values in measurements.

Comments

Data type

Binding

Codes specifying why the result (Observation.value[x]) is missing.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1, obs-6

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
v2: N/A
rim: value.nullFlavor

interpretation

0..*

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:genomic-hgvs.interpretation

Short description

High, low, normal, etc.

Alternate names

Abnormal Flag

Definition

A categorical assessment of an observation value. For example, high, low, normal.

Requirements

For some results, particularly numeric results, an interpretation is necessary to fully understand the significance of a result.

Comments

Data type

Binding

Codes identifying interpretations of observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
sct-concept: < 260245000 |Findings values|
v2: OBX-8
rim: interpretationCode
sct-attr: 363713009 |Has interpretation|

referenceRange

0..*

There are no (further) constraints on this element

Element id

Observation.component:genomic-hgvs.referenceRange

Short description

Provides guide for interpretation of component result

Definition

Guidance on how to interpret the value by comparison to a normal or recommended range.

Requirements

Knowing what values are considered "normal" can help evaluate the significance of a particular result. Need to be able to provide multiple reference ranges for different contexts.

Comments

Mappings

v2: OBX.7
rim: outboundRelationship[typeCode=REFV]/target[classCode=OBS, moodCode=EVN]

cytogenomic-nomenclature

0..1

There are no (further) constraints on this element

Element id

Observation.component:cytogenomic-nomenclature

Short description

Cytogenomic Nomenclature (ISCN)

Definition

Fully describes a variant with a single code. Typically a large variant such as a mosaic, abnormal chromosome numbers, etc.

Requirements

Comments

For a discussion on the ways Observations can be assembled in groups together see Notes below.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: containment by OBX-4?
rim: outBoundRelationship[typeCode=COMP]

0..1

There are no (further) constraints on this element

Element id

Observation.component:cytogenomic-nomenclature.id

Short description

Unique id for inter-element referencing

Definition

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Data type

Mappings

rim: n/a

extension

0..*

There are no (further) constraints on this element

Element id

Observation.component:cytogenomic-nomenclature.extension

Short description

Additional content defined by implementations

Alternate names

extensions, user content

Definition

Comments

Data type

Slicing

Unordered, Open, by url(Value)

Extensions are always sliced by (at least) url

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

modifierExtension

Σ ?! C

0..*

There are no (further) constraints on this element

Element id

Observation.component:cytogenomic-nomenclature.modifierExtension

Short description

Extensions that cannot be ignored even if unrecognized

Alternate names

extensions, user content, modifiers

Definition

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

Requirements

Comments

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

code

1..1

CodeableConceptPattern

There are no (further) constraints on this element

Element id

Observation.component:cytogenomic-nomenclature.code

Short description

81291-7

Definition

Describes what was observed. Sometimes this is called the observation "code".

Requirements

Knowing what kind of observation is being made is essential to understanding the observation.

Comments

All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

Data type

Binding

Codes identifying names of simple observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Pattern

{
  "coding": [
    {
      "system": "http://loinc.org",
      "code": "81291-7"
    }
  ]
}

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
w5: FiveWs.what[x]
sct-concept: < 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
v2: OBX-3
rim: code

value[x]

1..1

There are no (further) constraints on this element

Element id

Observation.component:cytogenomic-nomenclature.value[x]

Short description

Actual component result

Definition

The information determined as a result of making the observation, if the information has a simple value.

Requirements

An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

Comments

Binding

Binding not yet defined

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
sct-concept: 363714003 |Interprets| < 441742003 |Evaluation finding|
v2: OBX.2, OBX.5, OBX.6
rim: value
sct-attr: 363714003 |Interprets|

valueCodeableConcept

There are no (further) constraints on this element

Data type

dataAbsentReason

0..1

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:cytogenomic-nomenclature.dataAbsentReason

Short description

Why the component result is missing

Definition

Provides a reason why the expected value in the element Observation.component.value[x] is missing.

Requirements

For many results it is necessary to handle exceptional values in measurements.

Comments

Data type

Binding

Codes specifying why the result (Observation.value[x]) is missing.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1, obs-6

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
v2: N/A
rim: value.nullFlavor

interpretation

0..*

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:cytogenomic-nomenclature.interpretation

Short description

High, low, normal, etc.

Alternate names

Abnormal Flag

Definition

A categorical assessment of an observation value. For example, high, low, normal.

Requirements

For some results, particularly numeric results, an interpretation is necessary to fully understand the significance of a result.

Comments

Data type

Binding

Codes identifying interpretations of observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
sct-concept: < 260245000 |Findings values|
v2: OBX-8
rim: interpretationCode
sct-attr: 363713009 |Has interpretation|

referenceRange

0..*

There are no (further) constraints on this element

Element id

Observation.component:cytogenomic-nomenclature.referenceRange

Short description

Provides guide for interpretation of component result

Definition

Guidance on how to interpret the value by comparison to a normal or recommended range.

Requirements

Knowing what values are considered "normal" can help evaluate the significance of a particular result. Need to be able to provide multiple reference ranges for different contexts.

Comments

Mappings

v2: OBX.7
rim: outboundRelationship[typeCode=REFV]/target[classCode=OBS, moodCode=EVN]

genomic-ref-seq

S Σ

0..1

There are no (further) constraints on this element

Element id

Observation.component:genomic-ref-seq

Short description

Genomic Reference Sequence

Definition

ID of the genomic reference sequence, which includes transcribed and non transcribed stretches

Requirements

Comments

For a discussion on the ways Observations can be assembled in groups together see Notes below.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: containment by OBX-4?
rim: outBoundRelationship[typeCode=COMP]

0..1

There are no (further) constraints on this element

Element id

Observation.component:genomic-ref-seq.id

Short description

Unique id for inter-element referencing

Definition

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Data type

Mappings

rim: n/a

extension

0..*

There are no (further) constraints on this element

Element id

Observation.component:genomic-ref-seq.extension

Short description

Additional content defined by implementations

Alternate names

extensions, user content

Definition

Comments

Data type

Slicing

Unordered, Open, by url(Value)

Extensions are always sliced by (at least) url

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

modifierExtension

Σ ?! C

0..*

There are no (further) constraints on this element

Element id

Observation.component:genomic-ref-seq.modifierExtension

Short description

Extensions that cannot be ignored even if unrecognized

Alternate names

extensions, user content, modifiers

Definition

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

Requirements

Comments

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

code

1..1

CodeableConceptPattern

There are no (further) constraints on this element

Element id

Observation.component:genomic-ref-seq.code

Short description

48013-7

Definition

Describes what was observed. Sometimes this is called the observation "code".

Requirements

Knowing what kind of observation is being made is essential to understanding the observation.

Comments

All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

Data type

Binding

Codes identifying names of simple observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Pattern

{
  "coding": [
    {
      "system": "http://loinc.org",
      "code": "48013-7"
    }
  ]
}

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
w5: FiveWs.what[x]
sct-concept: < 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
v2: OBX-3
rim: code

value[x]

1..1

There are no (further) constraints on this element

Element id

Observation.component:genomic-ref-seq.value[x]

Short description

Versioned genomic reference sequence identifier

Definition

The information determined as a result of making the observation, if the information has a simple value.

Requirements

An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

Comments

Binding

Multiple bindings acceptable (NCBI or LRG)

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
sct-concept: 363714003 |Interprets| < 441742003 |Evaluation finding|
v2: OBX.2, OBX.5, OBX.6
rim: value
sct-attr: 363714003 |Interprets|

valueCodeableConcept

There are no (further) constraints on this element

Data type

dataAbsentReason

0..1

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:genomic-ref-seq.dataAbsentReason

Short description

Why the component result is missing

Definition

Provides a reason why the expected value in the element Observation.component.value[x] is missing.

Requirements

For many results it is necessary to handle exceptional values in measurements.

Comments

Data type

Binding

Codes specifying why the result (Observation.value[x]) is missing.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1, obs-6

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
v2: N/A
rim: value.nullFlavor

interpretation

0..*

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:genomic-ref-seq.interpretation

Short description

High, low, normal, etc.

Alternate names

Abnormal Flag

Definition

A categorical assessment of an observation value. For example, high, low, normal.

Requirements

For some results, particularly numeric results, an interpretation is necessary to fully understand the significance of a result.

Comments

Data type

Binding

Codes identifying interpretations of observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
sct-concept: < 260245000 |Findings values|
v2: OBX-8
rim: interpretationCode
sct-attr: 363713009 |Has interpretation|

referenceRange

0..*

There are no (further) constraints on this element

Element id

Observation.component:genomic-ref-seq.referenceRange

Short description

Provides guide for interpretation of component result

Definition

Guidance on how to interpret the value by comparison to a normal or recommended range.

Requirements

Knowing what values are considered "normal" can help evaluate the significance of a particular result. Need to be able to provide multiple reference ranges for different contexts.

Comments

Mappings

v2: OBX.7
rim: outboundRelationship[typeCode=REFV]/target[classCode=OBS, moodCode=EVN]

transcript-ref-seq

S Σ

0..1

There are no (further) constraints on this element

Element id

Observation.component:transcript-ref-seq

Short description

Reference Transcript

Definition

NCBI's RefSeq ('NM_...'), Ensembl ('ENST...'), and LRG ('LRG...' plus 't1' to indicate transcript)

Requirements

Comments

For a discussion on the ways Observations can be assembled in groups together see Notes below.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: containment by OBX-4?
rim: outBoundRelationship[typeCode=COMP]

0..1

There are no (further) constraints on this element

Element id

Observation.component:transcript-ref-seq.id

Short description

Unique id for inter-element referencing

Definition

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Data type

Mappings

rim: n/a

extension

0..*

There are no (further) constraints on this element

Element id

Observation.component:transcript-ref-seq.extension

Short description

Additional content defined by implementations

Alternate names

extensions, user content

Definition

Comments

Data type

Slicing

Unordered, Open, by url(Value)

Extensions are always sliced by (at least) url

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

modifierExtension

Σ ?! C

0..*

There are no (further) constraints on this element

Element id

Observation.component:transcript-ref-seq.modifierExtension

Short description

Extensions that cannot be ignored even if unrecognized

Alternate names

extensions, user content, modifiers

Definition

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

Requirements

Comments

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

code

1..1

CodeableConceptPattern

There are no (further) constraints on this element

Element id

Observation.component:transcript-ref-seq.code

Short description

51958-7

Definition

Describes what was observed. Sometimes this is called the observation "code".

Requirements

Knowing what kind of observation is being made is essential to understanding the observation.

Comments

All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

Data type

Binding

Codes identifying names of simple observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Pattern

{
  "coding": [
    {
      "system": "http://loinc.org",
      "code": "51958-7"
    }
  ]
}

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
w5: FiveWs.what[x]
sct-concept: < 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
v2: OBX-3
rim: code

value[x]

1..1

There are no (further) constraints on this element

Element id

Observation.component:transcript-ref-seq.value[x]

Short description

Versioned transcript reference sequence identifier

Definition

The information determined as a result of making the observation, if the information has a simple value.

Requirements

An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

Comments

Binding

Multiple bindings acceptable (NCBI or LRG)

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
sct-concept: 363714003 |Interprets| < 441742003 |Evaluation finding|
v2: OBX.2, OBX.5, OBX.6
rim: value
sct-attr: 363714003 |Interprets|

valueCodeableConcept

There are no (further) constraints on this element

Data type

dataAbsentReason

0..1

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:transcript-ref-seq.dataAbsentReason

Short description

Why the component result is missing

Definition

Provides a reason why the expected value in the element Observation.component.value[x] is missing.

Requirements

For many results it is necessary to handle exceptional values in measurements.

Comments

Data type

Binding

Codes specifying why the result (Observation.value[x]) is missing.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1, obs-6

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
v2: N/A
rim: value.nullFlavor

interpretation

0..*

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:transcript-ref-seq.interpretation

Short description

High, low, normal, etc.

Alternate names

Abnormal Flag

Definition

A categorical assessment of an observation value. For example, high, low, normal.

Requirements

For some results, particularly numeric results, an interpretation is necessary to fully understand the significance of a result.

Comments

Data type

Binding

Codes identifying interpretations of observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
sct-concept: < 260245000 |Findings values|
v2: OBX-8
rim: interpretationCode
sct-attr: 363713009 |Has interpretation|

referenceRange

0..*

There are no (further) constraints on this element

Element id

Observation.component:transcript-ref-seq.referenceRange

Short description

Provides guide for interpretation of component result

Definition

Guidance on how to interpret the value by comparison to a normal or recommended range.

Requirements

Knowing what values are considered "normal" can help evaluate the significance of a particular result. Need to be able to provide multiple reference ranges for different contexts.

Comments

Mappings

v2: OBX.7
rim: outboundRelationship[typeCode=REFV]/target[classCode=OBS, moodCode=EVN]

exact-start-end

S Σ

0..1

There are no (further) constraints on this element

Element id

Observation.component:exact-start-end

Short description

Exact Start-End

Definition

The exact integer-based genomic coordinates of the start and end of the variant region.

Requirements

Comments

For a discussion on the ways Observations can be assembled in groups together see Notes below.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: containment by OBX-4?
rim: outBoundRelationship[typeCode=COMP]

0..1

There are no (further) constraints on this element

Element id

Observation.component:exact-start-end.id

Short description

Unique id for inter-element referencing

Definition

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Data type

Mappings

rim: n/a

extension

0..*

There are no (further) constraints on this element

Element id

Observation.component:exact-start-end.extension

Short description

Additional content defined by implementations

Alternate names

extensions, user content

Definition

Comments

Data type

Slicing

Unordered, Open, by url(Value)

Extensions are always sliced by (at least) url

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

modifierExtension

Σ ?! C

0..*

There are no (further) constraints on this element

Element id

Observation.component:exact-start-end.modifierExtension

Short description

Extensions that cannot be ignored even if unrecognized

Alternate names

extensions, user content, modifiers

Definition

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

Requirements

Comments

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

code

1..1

CodeableConceptPattern

There are no (further) constraints on this element

Element id

Observation.component:exact-start-end.code

Short description

81254-5

Definition

Describes what was observed. Sometimes this is called the observation "code".

Requirements

Knowing what kind of observation is being made is essential to understanding the observation.

Comments

All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

Data type

Binding

Codes identifying names of simple observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Pattern

{
  "coding": [
    {
      "system": "http://loinc.org",
      "code": "81254-5"
    }
  ]
}

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
w5: FiveWs.what[x]
sct-concept: < 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
v2: OBX-3
rim: code

value[x]

0..1

There are no (further) constraints on this element

Element id

Observation.component:exact-start-end.value[x]

Short description

Range in question. 'High' can be omitted for single nucleotide variants.

Definition

The information determined as a result of making the observation, if the information has a simple value.

Requirements

An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

Comments

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
sct-concept: 363714003 |Interprets| < 441742003 |Evaluation finding|
v2: OBX.2, OBX.5, OBX.6
rim: value
sct-attr: 363714003 |Interprets|

valueRange

There are no (further) constraints on this element

Data type

dataAbsentReason

0..1

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:exact-start-end.dataAbsentReason

Short description

Why the component result is missing

Definition

Provides a reason why the expected value in the element Observation.component.value[x] is missing.

Requirements

For many results it is necessary to handle exceptional values in measurements.

Comments

Data type

Binding

Codes specifying why the result (Observation.value[x]) is missing.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1, obs-6

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
v2: N/A
rim: value.nullFlavor

interpretation

0..*

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:exact-start-end.interpretation

Short description

High, low, normal, etc.

Alternate names

Abnormal Flag

Definition

A categorical assessment of an observation value. For example, high, low, normal.

Requirements

For some results, particularly numeric results, an interpretation is necessary to fully understand the significance of a result.

Comments

Data type

Binding

Codes identifying interpretations of observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
sct-concept: < 260245000 |Findings values|
v2: OBX-8
rim: interpretationCode
sct-attr: 363713009 |Has interpretation|

referenceRange

0..*

There are no (further) constraints on this element

Element id

Observation.component:exact-start-end.referenceRange

Short description

Provides guide for interpretation of component result

Definition

Guidance on how to interpret the value by comparison to a normal or recommended range.

Requirements

Knowing what values are considered "normal" can help evaluate the significance of a particular result. Need to be able to provide multiple reference ranges for different contexts.

Comments

Mappings

v2: OBX.7
rim: outboundRelationship[typeCode=REFV]/target[classCode=OBS, moodCode=EVN]

inner-start-end

S Σ

0..1

There are no (further) constraints on this element

Element id

Observation.component:inner-start-end

Short description

Inner Start-End

Definition

The genomic coordinates of the narrowest genomic range in which the variant might reside. Used when the exact boundaries of the variant are not clear.

Requirements

Comments

For a discussion on the ways Observations can be assembled in groups together see Notes below.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: containment by OBX-4?
rim: outBoundRelationship[typeCode=COMP]

0..1

There are no (further) constraints on this element

Element id

Observation.component:inner-start-end.id

Short description

Unique id for inter-element referencing

Definition

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Data type

Mappings

rim: n/a

extension

0..*

There are no (further) constraints on this element

Element id

Observation.component:inner-start-end.extension

Short description

Additional content defined by implementations

Alternate names

extensions, user content

Definition

Comments

Data type

Slicing

Unordered, Open, by url(Value)

Extensions are always sliced by (at least) url

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

modifierExtension

Σ ?! C

0..*

There are no (further) constraints on this element

Element id

Observation.component:inner-start-end.modifierExtension

Short description

Extensions that cannot be ignored even if unrecognized

Alternate names

extensions, user content, modifiers

Definition

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

Requirements

Comments

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

code

1..1

CodeableConceptPattern

There are no (further) constraints on this element

Element id

Observation.component:inner-start-end.code

Short description

81302-2

Definition

Describes what was observed. Sometimes this is called the observation "code".

Requirements

Knowing what kind of observation is being made is essential to understanding the observation.

Comments

All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

Data type

Binding

Codes identifying names of simple observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Pattern

{
  "coding": [
    {
      "system": "http://loinc.org",
      "code": "81302-2"
    }
  ]
}

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
w5: FiveWs.what[x]
sct-concept: < 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
v2: OBX-3
rim: code

value[x]

0..1

There are no (further) constraints on this element

Element id

Observation.component:inner-start-end.value[x]

Short description

Imprecise variant inner-bounding range

Definition

The information determined as a result of making the observation, if the information has a simple value.

Requirements

An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

Comments

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
sct-concept: 363714003 |Interprets| < 441742003 |Evaluation finding|
v2: OBX.2, OBX.5, OBX.6
rim: value
sct-attr: 363714003 |Interprets|

valueRange

There are no (further) constraints on this element

Data type

dataAbsentReason

0..1

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:inner-start-end.dataAbsentReason

Short description

Why the component result is missing

Definition

Provides a reason why the expected value in the element Observation.component.value[x] is missing.

Requirements

For many results it is necessary to handle exceptional values in measurements.

Comments

Data type

Binding

Codes specifying why the result (Observation.value[x]) is missing.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1, obs-6

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
v2: N/A
rim: value.nullFlavor

interpretation

0..*

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:inner-start-end.interpretation

Short description

High, low, normal, etc.

Alternate names

Abnormal Flag

Definition

A categorical assessment of an observation value. For example, high, low, normal.

Requirements

For some results, particularly numeric results, an interpretation is necessary to fully understand the significance of a result.

Comments

Data type

Binding

Codes identifying interpretations of observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
sct-concept: < 260245000 |Findings values|
v2: OBX-8
rim: interpretationCode
sct-attr: 363713009 |Has interpretation|

referenceRange

0..*

There are no (further) constraints on this element

Element id

Observation.component:inner-start-end.referenceRange

Short description

Provides guide for interpretation of component result

Definition

Guidance on how to interpret the value by comparison to a normal or recommended range.

Requirements

Knowing what values are considered "normal" can help evaluate the significance of a particular result. Need to be able to provide multiple reference ranges for different contexts.

Comments

Mappings

v2: OBX.7
rim: outboundRelationship[typeCode=REFV]/target[classCode=OBS, moodCode=EVN]

outer-start-end

S Σ

0..1

There are no (further) constraints on this element

Element id

Observation.component:outer-start-end

Short description

Outer Start-End

Definition

The genomic coordinates of the widest genomic range in which the variant might reside. Used when the exact boundaries of the variant are not clear.

Requirements

Comments

For a discussion on the ways Observations can be assembled in groups together see Notes below.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: containment by OBX-4?
rim: outBoundRelationship[typeCode=COMP]

0..1

There are no (further) constraints on this element

Element id

Observation.component:outer-start-end.id

Short description

Unique id for inter-element referencing

Definition

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Data type

Mappings

rim: n/a

extension

0..*

There are no (further) constraints on this element

Element id

Observation.component:outer-start-end.extension

Short description

Additional content defined by implementations

Alternate names

extensions, user content

Definition

Comments

Data type

Slicing

Unordered, Open, by url(Value)

Extensions are always sliced by (at least) url

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

modifierExtension

Σ ?! C

0..*

There are no (further) constraints on this element

Element id

Observation.component:outer-start-end.modifierExtension

Short description

Extensions that cannot be ignored even if unrecognized

Alternate names

extensions, user content, modifiers

Definition

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

Requirements

Comments

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

code

1..1

CodeableConceptPattern

There are no (further) constraints on this element

Element id

Observation.component:outer-start-end.code

Short description

81301-4

Definition

Describes what was observed. Sometimes this is called the observation "code".

Requirements

Knowing what kind of observation is being made is essential to understanding the observation.

Comments

All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

Data type

Binding

Codes identifying names of simple observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Pattern

{
  "coding": [
    {
      "system": "http://loinc.org",
      "code": "81301-4"
    }
  ]
}

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
w5: FiveWs.what[x]
sct-concept: < 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
v2: OBX-3
rim: code

value[x]

0..1

There are no (further) constraints on this element

Element id

Observation.component:outer-start-end.value[x]

Short description

Imprecise variant outer-bounding range

Definition

The information determined as a result of making the observation, if the information has a simple value.

Requirements

An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

Comments

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
sct-concept: 363714003 |Interprets| < 441742003 |Evaluation finding|
v2: OBX.2, OBX.5, OBX.6
rim: value
sct-attr: 363714003 |Interprets|

valueRange

There are no (further) constraints on this element

Data type

dataAbsentReason

0..1

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:outer-start-end.dataAbsentReason

Short description

Why the component result is missing

Definition

Provides a reason why the expected value in the element Observation.component.value[x] is missing.

Requirements

For many results it is necessary to handle exceptional values in measurements.

Comments

Data type

Binding

Codes specifying why the result (Observation.value[x]) is missing.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1, obs-6

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
v2: N/A
rim: value.nullFlavor

interpretation

0..*

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:outer-start-end.interpretation

Short description

High, low, normal, etc.

Alternate names

Abnormal Flag

Definition

A categorical assessment of an observation value. For example, high, low, normal.

Requirements

For some results, particularly numeric results, an interpretation is necessary to fully understand the significance of a result.

Comments

Data type

Binding

Codes identifying interpretations of observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
sct-concept: < 260245000 |Findings values|
v2: OBX-8
rim: interpretationCode
sct-attr: 363713009 |Has interpretation|

referenceRange

0..*

There are no (further) constraints on this element

Element id

Observation.component:outer-start-end.referenceRange

Short description

Provides guide for interpretation of component result

Definition

Guidance on how to interpret the value by comparison to a normal or recommended range.

Requirements

Knowing what values are considered "normal" can help evaluate the significance of a particular result. Need to be able to provide multiple reference ranges for different contexts.

Comments

Mappings

v2: OBX.7
rim: outboundRelationship[typeCode=REFV]/target[classCode=OBS, moodCode=EVN]

coordinate-system

0..1

There are no (further) constraints on this element

Element id

Observation.component:coordinate-system

Short description

Coordinate System

Definition

These are different ways of identifying nucleotides or amino acids within a sequence. In the 1-based system, the first unit of the polymer (e.g. the first nucleotide) is counted as number 1. In the 0-based system, the number 0 designates the location before the first nucleotide. Different databases and file types may use different systems.

Requirements

Comments

For a discussion on the ways Observations can be assembled in groups together see Notes below.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: containment by OBX-4?
rim: outBoundRelationship[typeCode=COMP]

0..1

There are no (further) constraints on this element

Element id

Observation.component:coordinate-system.id

Short description

Unique id for inter-element referencing

Definition

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Data type

Mappings

rim: n/a

extension

0..*

There are no (further) constraints on this element

Element id

Observation.component:coordinate-system.extension

Short description

Additional content defined by implementations

Alternate names

extensions, user content

Definition

Comments

Data type

Slicing

Unordered, Open, by url(Value)

Extensions are always sliced by (at least) url

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

modifierExtension

Σ ?! C

0..*

There are no (further) constraints on this element

Element id

Observation.component:coordinate-system.modifierExtension

Short description

Extensions that cannot be ignored even if unrecognized

Alternate names

extensions, user content, modifiers

Definition

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

Requirements

Comments

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

code

1..1

CodeableConceptPattern

There are no (further) constraints on this element

Element id

Observation.component:coordinate-system.code

Short description

92822-6

Definition

Describes what was observed. Sometimes this is called the observation "code".

Requirements

Knowing what kind of observation is being made is essential to understanding the observation.

Comments

All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

Data type

Binding

Codes identifying names of simple observations.

http://loinc.org/vs/LL5323-2 (extensible)

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Pattern

{
  "coding": [
    {
      "system": "http://loinc.org",
      "code": "92822-6"
    }
  ]
}

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
w5: FiveWs.what[x]
sct-concept: < 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
v2: OBX-3
rim: code

value[x]

1..1

Binding

There are no (further) constraints on this element

Element id

Observation.component:coordinate-system.value[x]

Short description

0-based interval counting | 0-based character counting | 1-based character counting

Definition

The information determined as a result of making the observation, if the information has a simple value.

Requirements

An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

Comments

Binding

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
sct-concept: 363714003 |Interprets| < 441742003 |Evaluation finding|
v2: OBX.2, OBX.5, OBX.6
rim: value
sct-attr: 363714003 |Interprets|

valueCodeableConcept

There are no (further) constraints on this element

Data type

dataAbsentReason

0..1

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:coordinate-system.dataAbsentReason

Short description

Why the component result is missing

Definition

Provides a reason why the expected value in the element Observation.component.value[x] is missing.

Requirements

For many results it is necessary to handle exceptional values in measurements.

Comments

Data type

Binding

Codes specifying why the result (Observation.value[x]) is missing.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1, obs-6

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
v2: N/A
rim: value.nullFlavor

interpretation

0..*

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:coordinate-system.interpretation

Short description

High, low, normal, etc.

Alternate names

Abnormal Flag

Definition

A categorical assessment of an observation value. For example, high, low, normal.

Requirements

For some results, particularly numeric results, an interpretation is necessary to fully understand the significance of a result.

Comments

Data type

Binding

Codes identifying interpretations of observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
sct-concept: < 260245000 |Findings values|
v2: OBX-8
rim: interpretationCode
sct-attr: 363713009 |Has interpretation|

referenceRange

0..*

There are no (further) constraints on this element

Element id

Observation.component:coordinate-system.referenceRange

Short description

Provides guide for interpretation of component result

Definition

Guidance on how to interpret the value by comparison to a normal or recommended range.

Requirements

Knowing what values are considered "normal" can help evaluate the significance of a particular result. Need to be able to provide multiple reference ranges for different contexts.

Comments

Mappings

v2: OBX.7
rim: outboundRelationship[typeCode=REFV]/target[classCode=OBS, moodCode=EVN]

ref-allele

S Σ

0..1

There are no (further) constraints on this element

Element id

Observation.component:ref-allele

Short description

Genomic Ref Allele

Definition

Reference values ('normal') examined within the Reference Sequence.

Requirements

Comments

For a discussion on the ways Observations can be assembled in groups together see Notes below.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: containment by OBX-4?
rim: outBoundRelationship[typeCode=COMP]

0..1

There are no (further) constraints on this element

Element id

Observation.component:ref-allele.id

Short description

Unique id for inter-element referencing

Definition

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Data type

Mappings

rim: n/a

extension

0..*

There are no (further) constraints on this element

Element id

Observation.component:ref-allele.extension

Short description

Additional content defined by implementations

Alternate names

extensions, user content

Definition

Comments

Data type

Slicing

Unordered, Open, by url(Value)

Extensions are always sliced by (at least) url

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

modifierExtension

Σ ?! C

0..*

There are no (further) constraints on this element

Element id

Observation.component:ref-allele.modifierExtension

Short description

Extensions that cannot be ignored even if unrecognized

Alternate names

extensions, user content, modifiers

Definition

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

Requirements

Comments

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

code

1..1

CodeableConceptPattern

There are no (further) constraints on this element

Element id

Observation.component:ref-allele.code

Short description

69547-8

Definition

Describes what was observed. Sometimes this is called the observation "code".

Requirements

Knowing what kind of observation is being made is essential to understanding the observation.

Comments

All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

Data type

Binding

Codes identifying names of simple observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Pattern

{
  "coding": [
    {
      "system": "http://loinc.org",
      "code": "69547-8"
    }
  ]
}

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
w5: FiveWs.what[x]
sct-concept: < 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
v2: OBX-3
rim: code

value[x]

0..1

There are no (further) constraints on this element

Element id

Observation.component:ref-allele.value[x]

Short description

Normalized string per the VCF format.

Definition

The information determined as a result of making the observation, if the information has a simple value.

Requirements

An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

Comments

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
sct-concept: 363714003 |Interprets| < 441742003 |Evaluation finding|
v2: OBX.2, OBX.5, OBX.6
rim: value
sct-attr: 363714003 |Interprets|

valueString

There are no (further) constraints on this element

Data type

dataAbsentReason

0..1

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:ref-allele.dataAbsentReason

Short description

Why the component result is missing

Definition

Provides a reason why the expected value in the element Observation.component.value[x] is missing.

Requirements

For many results it is necessary to handle exceptional values in measurements.

Comments

Data type

Binding

Codes specifying why the result (Observation.value[x]) is missing.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1, obs-6

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
v2: N/A
rim: value.nullFlavor

interpretation

0..*

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:ref-allele.interpretation

Short description

High, low, normal, etc.

Alternate names

Abnormal Flag

Definition

A categorical assessment of an observation value. For example, high, low, normal.

Requirements

For some results, particularly numeric results, an interpretation is necessary to fully understand the significance of a result.

Comments

Data type

Binding

Codes identifying interpretations of observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
sct-concept: < 260245000 |Findings values|
v2: OBX-8
rim: interpretationCode
sct-attr: 363713009 |Has interpretation|

referenceRange

0..*

There are no (further) constraints on this element

Element id

Observation.component:ref-allele.referenceRange

Short description

Provides guide for interpretation of component result

Definition

Guidance on how to interpret the value by comparison to a normal or recommended range.

Requirements

Knowing what values are considered "normal" can help evaluate the significance of a particular result. Need to be able to provide multiple reference ranges for different contexts.

Comments

Mappings

v2: OBX.7
rim: outboundRelationship[typeCode=REFV]/target[classCode=OBS, moodCode=EVN]

alt-allele

S Σ

0..1

There are no (further) constraints on this element

Element id

Observation.component:alt-allele

Short description

Genomic Alt Allele

Definition

The genomic alternate allele is the contiguous segment of DNA in the test sample that differs from the reference allele at the same location and thus defines a variant.

Requirements

Comments

For a discussion on the ways Observations can be assembled in groups together see Notes below.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: containment by OBX-4?
rim: outBoundRelationship[typeCode=COMP]

0..1

There are no (further) constraints on this element

Element id

Observation.component:alt-allele.id

Short description

Unique id for inter-element referencing

Definition

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Data type

Mappings

rim: n/a

extension

0..*

There are no (further) constraints on this element

Element id

Observation.component:alt-allele.extension

Short description

Additional content defined by implementations

Alternate names

extensions, user content

Definition

Comments

Data type

Slicing

Unordered, Open, by url(Value)

Extensions are always sliced by (at least) url

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

modifierExtension

Σ ?! C

0..*

There are no (further) constraints on this element

Element id

Observation.component:alt-allele.modifierExtension

Short description

Extensions that cannot be ignored even if unrecognized

Alternate names

extensions, user content, modifiers

Definition

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

Requirements

Comments

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

code

1..1

CodeableConceptPattern

There are no (further) constraints on this element

Element id

Observation.component:alt-allele.code

Short description

69551-0

Definition

Describes what was observed. Sometimes this is called the observation "code".

Requirements

Knowing what kind of observation is being made is essential to understanding the observation.

Comments

All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

Data type

Binding

Codes identifying names of simple observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Pattern

{
  "coding": [
    {
      "system": "http://loinc.org",
      "code": "69551-0"
    }
  ]
}

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
w5: FiveWs.what[x]
sct-concept: < 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
v2: OBX-3
rim: code

value[x]

0..1

There are no (further) constraints on this element

Element id

Observation.component:alt-allele.value[x]

Short description

Normalized string per the VCF format.

Definition

The information determined as a result of making the observation, if the information has a simple value.

Requirements

An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

Comments

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
sct-concept: 363714003 |Interprets| < 441742003 |Evaluation finding|
v2: OBX.2, OBX.5, OBX.6
rim: value
sct-attr: 363714003 |Interprets|

valueString

There are no (further) constraints on this element

Data type

dataAbsentReason

0..1

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:alt-allele.dataAbsentReason

Short description

Why the component result is missing

Definition

Provides a reason why the expected value in the element Observation.component.value[x] is missing.

Requirements

For many results it is necessary to handle exceptional values in measurements.

Comments

Data type

Binding

Codes specifying why the result (Observation.value[x]) is missing.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1, obs-6

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
v2: N/A
rim: value.nullFlavor

interpretation

0..*

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:alt-allele.interpretation

Short description

High, low, normal, etc.

Alternate names

Abnormal Flag

Definition

A categorical assessment of an observation value. For example, high, low, normal.

Requirements

For some results, particularly numeric results, an interpretation is necessary to fully understand the significance of a result.

Comments

Data type

Binding

Codes identifying interpretations of observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
sct-concept: < 260245000 |Findings values|
v2: OBX-8
rim: interpretationCode
sct-attr: 363713009 |Has interpretation|

referenceRange

0..*

There are no (further) constraints on this element

Element id

Observation.component:alt-allele.referenceRange

Short description

Provides guide for interpretation of component result

Definition

Guidance on how to interpret the value by comparison to a normal or recommended range.

Requirements

Knowing what values are considered "normal" can help evaluate the significance of a particular result. Need to be able to provide multiple reference ranges for different contexts.

Comments

Mappings

v2: OBX.7
rim: outboundRelationship[typeCode=REFV]/target[classCode=OBS, moodCode=EVN]

coding-change-type

S Σ

0..1

There are no (further) constraints on this element

Element id

Observation.component:coding-change-type

Short description

Coding DNA Change Type

Definition

Type of DNA change observed. Convenience property for variants with exact breakpoints, required otherwise.

Requirements

Comments

For a discussion on the ways Observations can be assembled in groups together see Notes below.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: containment by OBX-4?
rim: outBoundRelationship[typeCode=COMP]

0..1

There are no (further) constraints on this element

Element id

Observation.component:coding-change-type.id

Short description

Unique id for inter-element referencing

Definition

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Data type

Mappings

rim: n/a

extension

0..*

There are no (further) constraints on this element

Element id

Observation.component:coding-change-type.extension

Short description

Additional content defined by implementations

Alternate names

extensions, user content

Definition

Comments

Data type

Slicing

Unordered, Open, by url(Value)

Extensions are always sliced by (at least) url

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

modifierExtension

Σ ?! C

0..*

There are no (further) constraints on this element

Element id

Observation.component:coding-change-type.modifierExtension

Short description

Extensions that cannot be ignored even if unrecognized

Alternate names

extensions, user content, modifiers

Definition

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

Requirements

Comments

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

code

1..1

CodeableConceptPattern

There are no (further) constraints on this element

Element id

Observation.component:coding-change-type.code

Short description

48019-4

Definition

Describes what was observed. Sometimes this is called the observation "code".

Requirements

Knowing what kind of observation is being made is essential to understanding the observation.

Comments

All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

Data type

Binding

Codes identifying names of simple observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Pattern

{
  "coding": [
    {
      "system": "http://loinc.org",
      "code": "48019-4"
    }
  ]
}

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
w5: FiveWs.what[x]
sct-concept: < 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
v2: OBX-3
rim: code

value[x]

1..1

Binding

There are no (further) constraints on this element

Element id

Observation.component:coding-change-type.value[x]

Short description

Definition

The information determined as a result of making the observation, if the information has a simple value.

Requirements

An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

Comments

Binding

Concepts in sequence ontology under SO:0002072

DNAChangeTypeVS (extensible)

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
sct-concept: 363714003 |Interprets| < 441742003 |Evaluation finding|
v2: OBX.2, OBX.5, OBX.6
rim: value
sct-attr: 363714003 |Interprets|

valueCodeableConcept

There are no (further) constraints on this element

Data type

dataAbsentReason

0..1

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:coding-change-type.dataAbsentReason

Short description

Why the component result is missing

Definition

Provides a reason why the expected value in the element Observation.component.value[x] is missing.

Requirements

For many results it is necessary to handle exceptional values in measurements.

Comments

Data type

Binding

Codes specifying why the result (Observation.value[x]) is missing.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1, obs-6

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
v2: N/A
rim: value.nullFlavor

interpretation

0..*

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:coding-change-type.interpretation

Short description

High, low, normal, etc.

Alternate names

Abnormal Flag

Definition

A categorical assessment of an observation value. For example, high, low, normal.

Requirements

For some results, particularly numeric results, an interpretation is necessary to fully understand the significance of a result.

Comments

Data type

Binding

Codes identifying interpretations of observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
sct-concept: < 260245000 |Findings values|
v2: OBX-8
rim: interpretationCode
sct-attr: 363713009 |Has interpretation|

referenceRange

0..*

There are no (further) constraints on this element

Element id

Observation.component:coding-change-type.referenceRange

Short description

Provides guide for interpretation of component result

Definition

Guidance on how to interpret the value by comparison to a normal or recommended range.

Requirements

Knowing what values are considered "normal" can help evaluate the significance of a particular result. Need to be able to provide multiple reference ranges for different contexts.

Comments

Mappings

v2: OBX.7
rim: outboundRelationship[typeCode=REFV]/target[classCode=OBS, moodCode=EVN]

genomic-source-class

S Σ

0..1

There are no (further) constraints on this element

Element id

Observation.component:genomic-source-class

Short description

Genomic Source Class

Definition

The genomic class of the specimen being analyzed: Germline for inherited genome, somatic for cancer genome, and prenatal for fetal genome.

Requirements

Comments

For a discussion on the ways Observations can be assembled in groups together see Notes below.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: containment by OBX-4?
rim: outBoundRelationship[typeCode=COMP]

0..1

There are no (further) constraints on this element

Element id

Observation.component:genomic-source-class.id

Short description

Unique id for inter-element referencing

Definition

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Data type

Mappings

rim: n/a

extension

0..*

There are no (further) constraints on this element

Element id

Observation.component:genomic-source-class.extension

Short description

Additional content defined by implementations

Alternate names

extensions, user content

Definition

Comments

Data type

Slicing

Unordered, Open, by url(Value)

Extensions are always sliced by (at least) url

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

modifierExtension

Σ ?! C

0..*

There are no (further) constraints on this element

Element id

Observation.component:genomic-source-class.modifierExtension

Short description

Extensions that cannot be ignored even if unrecognized

Alternate names

extensions, user content, modifiers

Definition

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

Requirements

Comments

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

code

1..1

CodeableConceptPattern

There are no (further) constraints on this element

Element id

Observation.component:genomic-source-class.code

Short description

48002-0

Definition

Describes what was observed. Sometimes this is called the observation "code".

Requirements

Knowing what kind of observation is being made is essential to understanding the observation.

Comments

All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

Data type

Binding

Codes identifying names of simple observations.

http://loinc.org/vs/LL378-1 (extensible)

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Pattern

{
  "coding": [
    {
      "system": "http://loinc.org",
      "code": "48002-0"
    }
  ]
}

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
w5: FiveWs.what[x]
sct-concept: < 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
v2: OBX-3
rim: code

value[x]

1..1

Binding

There are no (further) constraints on this element

Element id

Observation.component:genomic-source-class.value[x]

Short description

Definition

The information determined as a result of making the observation, if the information has a simple value.

Requirements

An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

Comments

Binding

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
sct-concept: 363714003 |Interprets| < 441742003 |Evaluation finding|
v2: OBX.2, OBX.5, OBX.6
rim: value
sct-attr: 363714003 |Interprets|

valueCodeableConcept

There are no (further) constraints on this element

Data type

dataAbsentReason

0..1

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:genomic-source-class.dataAbsentReason

Short description

Why the component result is missing

Definition

Provides a reason why the expected value in the element Observation.component.value[x] is missing.

Requirements

For many results it is necessary to handle exceptional values in measurements.

Comments

Data type

Binding

Codes specifying why the result (Observation.value[x]) is missing.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1, obs-6

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
v2: N/A
rim: value.nullFlavor

interpretation

0..*

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:genomic-source-class.interpretation

Short description

High, low, normal, etc.

Alternate names

Abnormal Flag

Definition

A categorical assessment of an observation value. For example, high, low, normal.

Requirements

For some results, particularly numeric results, an interpretation is necessary to fully understand the significance of a result.

Comments

Data type

Binding

Codes identifying interpretations of observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
sct-concept: < 260245000 |Findings values|
v2: OBX-8
rim: interpretationCode
sct-attr: 363713009 |Has interpretation|

referenceRange

0..*

There are no (further) constraints on this element

Element id

Observation.component:genomic-source-class.referenceRange

Short description

Provides guide for interpretation of component result

Definition

Guidance on how to interpret the value by comparison to a normal or recommended range.

Requirements

Knowing what values are considered "normal" can help evaluate the significance of a particular result. Need to be able to provide multiple reference ranges for different contexts.

Comments

Mappings

v2: OBX.7
rim: outboundRelationship[typeCode=REFV]/target[classCode=OBS, moodCode=EVN]

sample-allelic-frequency

S Σ

0..1

There are no (further) constraints on this element

Element id

Observation.component:sample-allelic-frequency

Short description

Sample Allelic Frequency

Definition

The relative frequency of the allele at a given locus in the sample.

Requirements

Comments

For a discussion on the ways Observations can be assembled in groups together see Notes below.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: containment by OBX-4?
rim: outBoundRelationship[typeCode=COMP]

0..1

There are no (further) constraints on this element

Element id

Observation.component:sample-allelic-frequency.id

Short description

Unique id for inter-element referencing

Definition

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Data type

Mappings

rim: n/a

extension

0..*

There are no (further) constraints on this element

Element id

Observation.component:sample-allelic-frequency.extension

Short description

Additional content defined by implementations

Alternate names

extensions, user content

Definition

Comments

Data type

Slicing

Unordered, Open, by url(Value)

Extensions are always sliced by (at least) url

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

modifierExtension

Σ ?! C

0..*

There are no (further) constraints on this element

Element id

Observation.component:sample-allelic-frequency.modifierExtension

Short description

Extensions that cannot be ignored even if unrecognized

Alternate names

extensions, user content, modifiers

Definition

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

Requirements

Comments

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

code

1..1

CodeableConceptPattern

There are no (further) constraints on this element

Element id

Observation.component:sample-allelic-frequency.code

Short description

81258-6

Definition

Describes what was observed. Sometimes this is called the observation "code".

Requirements

Knowing what kind of observation is being made is essential to understanding the observation.

Comments

All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

Data type

Binding

Codes identifying names of simple observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Pattern

{
  "coding": [
    {
      "system": "http://loinc.org",
      "code": "81258-6"
    }
  ]
}

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
w5: FiveWs.what[x]
sct-concept: < 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
v2: OBX-3
rim: code

value[x]

0..1

There are no (further) constraints on this element

Element id

Observation.component:sample-allelic-frequency.value[x]

Short description

Relative frequency in the sample

Definition

The information determined as a result of making the observation, if the information has a simple value.

Requirements

An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

Comments

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
sct-concept: 363714003 |Interprets| < 441742003 |Evaluation finding|
v2: OBX.2, OBX.5, OBX.6
rim: value
sct-attr: 363714003 |Interprets|

0..1

There are no (further) constraints on this element

Element id

Observation.component:sample-allelic-frequency.value[x].id

Short description

Unique id for inter-element referencing

Definition

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Data type

Mappings

rim: n/a

extension

0..*

There are no (further) constraints on this element

Element id

Observation.component:sample-allelic-frequency.value[x].extension

Short description

Additional content defined by implementations

Alternate names

extensions, user content

Definition

Comments

Data type

Slicing

Unordered, Open, by url(Value)

Extensions are always sliced by (at least) url

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

value

0..1

decimal

There are no (further) constraints on this element

Element id

Observation.component:sample-allelic-frequency.value[x].value

Short description

Numerical value (with implicit precision)

Definition

The value of the measured amount. The value includes an implicit precision in the presentation of the value.

Requirements

Precision is handled implicitly in almost all cases of measurement.

Comments

The implicit precision in the value should always be honored. Monetary values have their own rules for handling precision (refer to standard accounting text books).

Data type

decimal

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: SN.2 / CQ - N/A
rim: PQ.value, CO.value, MO.value, IVL.high or IVL.low depending on the value

comparator

Σ ?!

0..1

codeBinding

There are no (further) constraints on this element

Element id

Observation.component:sample-allelic-frequency.value[x].comparator

Short description

< | <= | >= | > - how to understand the value

Definition

How the value should be understood and represented - whether the actual value is greater or less than the stated value due to measurement issues; e.g. if the comparator is "<" , then the real value is < stated value.

Requirements

Need a framework for handling measures where the value is <5ug/L or >400mg/L due to the limitations of measuring methodology.

Comments

Note that FHIR strings SHALL NOT exceed 1MB in size

Meaning when missing

If there is no comparator, then there is no modification of the value

Data type

Binding

How the Quantity should be understood and represented.

QuantityComparator (required)

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: SN.1 / CQ.1
rim: IVL properties

unit

0..1

There are no (further) constraints on this element

Element id

Observation.component:sample-allelic-frequency.value[x].unit

Short description

Unit representation

Definition

A human-readable form of the unit.

Requirements

There are many representations for units of measure and in many contexts, particular representations are fixed and required. I.e. mcg for micrograms.

Comments

Note that FHIR strings SHALL NOT exceed 1MB in size

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: (see OBX.6 etc.) / CQ.2
rim: PQ.unit

system

Σ C

0..1

uriPattern

There are no (further) constraints on this element

Element id

Observation.component:sample-allelic-frequency.value[x].system

Short description

System that defines coded unit form

Definition

The identification of the system that provides the coded form of the unit.

Requirements

Need to know the system that defines the coded form of the unit.

Comments

see http://en.wikipedia.org/wiki/Uniform_resource_identifier

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1, qty-3

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Pattern

http://unitsofmeasure.org

Mappings

rim: n/a
v2: (see OBX.6 etc.) / CQ.2
rim: CO.codeSystem, PQ.translation.codeSystem

code

0..1

There are no (further) constraints on this element

Element id

Observation.component:sample-allelic-frequency.value[x].code

Short description

Coded form of the unit

Definition

A computer processable form of the unit in some unit representation system.

Requirements

Need a computable form of the unit that is fixed across all forms. UCUM provides this for quantities, but SNOMED CT provides many units of interest.

Comments

The preferred system is UCUM, but SNOMED CT can also be used (for customary units) or ISO 4217 for currency. The context of use may additionally require a code from a particular system.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: (see OBX.6 etc.) / CQ.2
rim: PQ.code, MO.currency, PQ.translation.code

dataAbsentReason

0..1

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:sample-allelic-frequency.dataAbsentReason

Short description

Why the component result is missing

Definition

Provides a reason why the expected value in the element Observation.component.value[x] is missing.

Requirements

For many results it is necessary to handle exceptional values in measurements.

Comments

Data type

Binding

Codes specifying why the result (Observation.value[x]) is missing.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1, obs-6

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
v2: N/A
rim: value.nullFlavor

interpretation

0..*

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:sample-allelic-frequency.interpretation

Short description

High, low, normal, etc.

Alternate names

Abnormal Flag

Definition

A categorical assessment of an observation value. For example, high, low, normal.

Requirements

For some results, particularly numeric results, an interpretation is necessary to fully understand the significance of a result.

Comments

Data type

Binding

Codes identifying interpretations of observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
sct-concept: < 260245000 |Findings values|
v2: OBX-8
rim: interpretationCode
sct-attr: 363713009 |Has interpretation|

referenceRange

0..*

There are no (further) constraints on this element

Element id

Observation.component:sample-allelic-frequency.referenceRange

Short description

Provides guide for interpretation of component result

Definition

Guidance on how to interpret the value by comparison to a normal or recommended range.

Requirements

Knowing what values are considered "normal" can help evaluate the significance of a particular result. Need to be able to provide multiple reference ranges for different contexts.

Comments

Mappings

v2: OBX.7
rim: outboundRelationship[typeCode=REFV]/target[classCode=OBS, moodCode=EVN]

allelic-read-depth

S Σ

0..1

There are no (further) constraints on this element

Element id

Observation.component:allelic-read-depth

Short description

Allelic Read Depth

Definition

Specifies the number of reads that identified the allele in question whether it consists of one or a small sequence of contiguous nucleotides. Different methods and purposes require different numbers of reads to be acceptable. Often >400, sometimes as few as 2-4.

Requirements

Comments

For a discussion on the ways Observations can be assembled in groups together see Notes below.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: containment by OBX-4?
rim: outBoundRelationship[typeCode=COMP]

0..1

There are no (further) constraints on this element

Element id

Observation.component:allelic-read-depth.id

Short description

Unique id for inter-element referencing

Definition

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Data type

Mappings

rim: n/a

extension

0..*

There are no (further) constraints on this element

Element id

Observation.component:allelic-read-depth.extension

Short description

Additional content defined by implementations

Alternate names

extensions, user content

Definition

Comments

Data type

Slicing

Unordered, Open, by url(Value)

Extensions are always sliced by (at least) url

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

modifierExtension

Σ ?! C

0..*

There are no (further) constraints on this element

Element id

Observation.component:allelic-read-depth.modifierExtension

Short description

Extensions that cannot be ignored even if unrecognized

Alternate names

extensions, user content, modifiers

Definition

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

Requirements

Comments

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

code

1..1

CodeableConceptPattern

There are no (further) constraints on this element

Element id

Observation.component:allelic-read-depth.code

Short description

82121-5

Definition

Describes what was observed. Sometimes this is called the observation "code".

Requirements

Knowing what kind of observation is being made is essential to understanding the observation.

Comments

All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

Data type

Binding

Codes identifying names of simple observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Pattern

{
  "coding": [
    {
      "system": "http://loinc.org",
      "code": "82121-5"
    }
  ]
}

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
w5: FiveWs.what[x]
sct-concept: < 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
v2: OBX-3
rim: code

value[x]

0..1

There are no (further) constraints on this element

Element id

Observation.component:allelic-read-depth.value[x]

Short description

Unfiltered count of supporting reads

Definition

The information determined as a result of making the observation, if the information has a simple value.

Requirements

An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

Comments

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
sct-concept: 363714003 |Interprets| < 441742003 |Evaluation finding|
v2: OBX.2, OBX.5, OBX.6
rim: value
sct-attr: 363714003 |Interprets|

valueQuantity

There are no (further) constraints on this element

Data type

dataAbsentReason

0..1

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:allelic-read-depth.dataAbsentReason

Short description

Why the component result is missing

Definition

Provides a reason why the expected value in the element Observation.component.value[x] is missing.

Requirements

For many results it is necessary to handle exceptional values in measurements.

Comments

Data type

Binding

Codes specifying why the result (Observation.value[x]) is missing.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1, obs-6

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
v2: N/A
rim: value.nullFlavor

interpretation

0..*

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:allelic-read-depth.interpretation

Short description

High, low, normal, etc.

Alternate names

Abnormal Flag

Definition

A categorical assessment of an observation value. For example, high, low, normal.

Requirements

For some results, particularly numeric results, an interpretation is necessary to fully understand the significance of a result.

Comments

Data type

Binding

Codes identifying interpretations of observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
sct-concept: < 260245000 |Findings values|
v2: OBX-8
rim: interpretationCode
sct-attr: 363713009 |Has interpretation|

referenceRange

0..*

There are no (further) constraints on this element

Element id

Observation.component:allelic-read-depth.referenceRange

Short description

Provides guide for interpretation of component result

Definition

Guidance on how to interpret the value by comparison to a normal or recommended range.

Requirements

Knowing what values are considered "normal" can help evaluate the significance of a particular result. Need to be able to provide multiple reference ranges for different contexts.

Comments

Mappings

v2: OBX.7
rim: outboundRelationship[typeCode=REFV]/target[classCode=OBS, moodCode=EVN]

allelic-state

S Σ

0..1

There are no (further) constraints on this element

Element id

Observation.component:allelic-state

Short description

Allelic State

Definition

The observed level of occurrence of the variant in the set of chromosomes.

Requirements

Comments

For a discussion on the ways Observations can be assembled in groups together see Notes below.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: containment by OBX-4?
rim: outBoundRelationship[typeCode=COMP]

0..1

There are no (further) constraints on this element

Element id

Observation.component:allelic-state.id

Short description

Unique id for inter-element referencing

Definition

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Data type

Mappings

rim: n/a

extension

0..*

There are no (further) constraints on this element

Element id

Observation.component:allelic-state.extension

Short description

Additional content defined by implementations

Alternate names

extensions, user content

Definition

Comments

Data type

Slicing

Unordered, Open, by url(Value)

Extensions are always sliced by (at least) url

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

modifierExtension

Σ ?! C

0..*

There are no (further) constraints on this element

Element id

Observation.component:allelic-state.modifierExtension

Short description

Extensions that cannot be ignored even if unrecognized

Alternate names

extensions, user content, modifiers

Definition

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

Requirements

Comments

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

code

1..1

CodeableConceptPattern

There are no (further) constraints on this element

Element id

Observation.component:allelic-state.code

Short description

53034-5

Definition

Describes what was observed. Sometimes this is called the observation "code".

Requirements

Knowing what kind of observation is being made is essential to understanding the observation.

Comments

All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

Data type

Binding

Codes identifying names of simple observations.

http://loinc.org/vs/LL381-5 (extensible)

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Pattern

{
  "coding": [
    {
      "system": "http://loinc.org",
      "code": "53034-5"
    }
  ]
}

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
w5: FiveWs.what[x]
sct-concept: < 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
v2: OBX-3
rim: code

value[x]

1..1

Binding

There are no (further) constraints on this element

Element id

Observation.component:allelic-state.value[x]

Short description

Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous

Definition

The information determined as a result of making the observation, if the information has a simple value.

Requirements

An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

Comments

Binding

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
sct-concept: 363714003 |Interprets| < 441742003 |Evaluation finding|
v2: OBX.2, OBX.5, OBX.6
rim: value
sct-attr: 363714003 |Interprets|

valueCodeableConcept

There are no (further) constraints on this element

Data type

dataAbsentReason

0..1

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:allelic-state.dataAbsentReason

Short description

Why the component result is missing

Definition

Provides a reason why the expected value in the element Observation.component.value[x] is missing.

Requirements

For many results it is necessary to handle exceptional values in measurements.

Comments

Data type

Binding

Codes specifying why the result (Observation.value[x]) is missing.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1, obs-6

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
v2: N/A
rim: value.nullFlavor

interpretation

0..*

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:allelic-state.interpretation

Short description

High, low, normal, etc.

Alternate names

Abnormal Flag

Definition

A categorical assessment of an observation value. For example, high, low, normal.

Requirements

For some results, particularly numeric results, an interpretation is necessary to fully understand the significance of a result.

Comments

Data type

Binding

Codes identifying interpretations of observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
sct-concept: < 260245000 |Findings values|
v2: OBX-8
rim: interpretationCode
sct-attr: 363713009 |Has interpretation|

referenceRange

0..*

There are no (further) constraints on this element

Element id

Observation.component:allelic-state.referenceRange

Short description

Provides guide for interpretation of component result

Definition

Guidance on how to interpret the value by comparison to a normal or recommended range.

Requirements

Knowing what values are considered "normal" can help evaluate the significance of a particular result. Need to be able to provide multiple reference ranges for different contexts.

Comments

Mappings

v2: OBX.7
rim: outboundRelationship[typeCode=REFV]/target[classCode=OBS, moodCode=EVN]

variant-inheritance

S Σ

0..1

There are no (further) constraints on this element

Element id

Observation.component:variant-inheritance

Short description

Variant Inheritance

Definition

By which parent the variant was inherited in the patient, if known.

Requirements

Comments

For a discussion on the ways Observations can be assembled in groups together see Notes below.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: containment by OBX-4?
rim: outBoundRelationship[typeCode=COMP]

0..1

There are no (further) constraints on this element

Element id

Observation.component:variant-inheritance.id

Short description

Unique id for inter-element referencing

Definition

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Data type

Mappings

rim: n/a

extension

0..*

There are no (further) constraints on this element

Element id

Observation.component:variant-inheritance.extension

Short description

Additional content defined by implementations

Alternate names

extensions, user content

Definition

Comments

Data type

Slicing

Unordered, Open, by url(Value)

Extensions are always sliced by (at least) url

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

modifierExtension

Σ ?! C

0..*

There are no (further) constraints on this element

Element id

Observation.component:variant-inheritance.modifierExtension

Short description

Extensions that cannot be ignored even if unrecognized

Alternate names

extensions, user content, modifiers

Definition

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

Requirements

Comments

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

code

1..1

CodeableConceptPattern

There are no (further) constraints on this element

Element id

Observation.component:variant-inheritance.code

Short description

variant-inheritance

Definition

Describes what was observed. Sometimes this is called the observation "code".

Requirements

Knowing what kind of observation is being made is essential to understanding the observation.

Comments

All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

Data type

Binding

Codes identifying names of simple observations.

VariantInheritanceVS (extensible)

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Pattern

{
  "coding": [
    {
      "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
      "code": "variant-inheritance"
    }
  ]
}

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
w5: FiveWs.what[x]
sct-concept: < 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
v2: OBX-3
rim: code

value[x]

1..1

Binding

There are no (further) constraints on this element

Element id

Observation.component:variant-inheritance.value[x]

Short description

Maternal | Paternal | Unknown

Definition

The information determined as a result of making the observation, if the information has a simple value.

Requirements

An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

Comments

Binding

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
sct-concept: 363714003 |Interprets| < 441742003 |Evaluation finding|
v2: OBX.2, OBX.5, OBX.6
rim: value
sct-attr: 363714003 |Interprets|

valueCodeableConcept

There are no (further) constraints on this element

Data type

dataAbsentReason

0..1

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:variant-inheritance.dataAbsentReason

Short description

Why the component result is missing

Definition

Provides a reason why the expected value in the element Observation.component.value[x] is missing.

Requirements

For many results it is necessary to handle exceptional values in measurements.

Comments

Data type

Binding

Codes specifying why the result (Observation.value[x]) is missing.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1, obs-6

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
v2: N/A
rim: value.nullFlavor

interpretation

0..*

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:variant-inheritance.interpretation

Short description

High, low, normal, etc.

Alternate names

Abnormal Flag

Definition

A categorical assessment of an observation value. For example, high, low, normal.

Requirements

For some results, particularly numeric results, an interpretation is necessary to fully understand the significance of a result.

Comments

Data type

Binding

Codes identifying interpretations of observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
sct-concept: < 260245000 |Findings values|
v2: OBX-8
rim: interpretationCode
sct-attr: 363713009 |Has interpretation|

referenceRange

0..*

There are no (further) constraints on this element

Element id

Observation.component:variant-inheritance.referenceRange

Short description

Provides guide for interpretation of component result

Definition

Guidance on how to interpret the value by comparison to a normal or recommended range.

Requirements

Knowing what values are considered "normal" can help evaluate the significance of a particular result. Need to be able to provide multiple reference ranges for different contexts.

Comments

Mappings

v2: OBX.7
rim: outboundRelationship[typeCode=REFV]/target[classCode=OBS, moodCode=EVN]

variation-code

S Σ

0..*

There are no (further) constraints on this element

Element id

Observation.component:variation-code

Short description

Variation Code

Definition

Accession number in a variant database such as ClinVar, given for cross-reference.

Requirements

Comments

For a discussion on the ways Observations can be assembled in groups together see Notes below.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: containment by OBX-4?
rim: outBoundRelationship[typeCode=COMP]

0..1

There are no (further) constraints on this element

Element id

Observation.component:variation-code.id

Short description

Unique id for inter-element referencing

Definition

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Data type

Mappings

rim: n/a

extension

0..*

There are no (further) constraints on this element

Element id

Observation.component:variation-code.extension

Short description

Additional content defined by implementations

Alternate names

extensions, user content

Definition

Comments

Data type

Slicing

Unordered, Open, by url(Value)

Extensions are always sliced by (at least) url

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

modifierExtension

Σ ?! C

0..*

There are no (further) constraints on this element

Element id

Observation.component:variation-code.modifierExtension

Short description

Extensions that cannot be ignored even if unrecognized

Alternate names

extensions, user content, modifiers

Definition

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

Requirements

Comments

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

code

1..1

CodeableConceptPattern

There are no (further) constraints on this element

Element id

Observation.component:variation-code.code

Short description

81252-9

Definition

Describes what was observed. Sometimes this is called the observation "code".

Requirements

Knowing what kind of observation is being made is essential to understanding the observation.

Comments

All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

Data type

Binding

Codes identifying names of simple observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Pattern

{
  "coding": [
    {
      "system": "http://loinc.org",
      "code": "81252-9"
    }
  ]
}

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
w5: FiveWs.what[x]
sct-concept: < 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
v2: OBX-3
rim: code

value[x]

1..1

There are no (further) constraints on this element

Element id

Observation.component:variation-code.value[x]

Short description

ClinVar ID or similar

Definition

The information determined as a result of making the observation, if the information has a simple value.

Requirements

An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

Comments

Binding

Multiple bindings acceptable

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
sct-concept: 363714003 |Interprets| < 441742003 |Evaluation finding|
v2: OBX.2, OBX.5, OBX.6
rim: value
sct-attr: 363714003 |Interprets|

valueCodeableConcept

There are no (further) constraints on this element

Data type

dataAbsentReason

0..1

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:variation-code.dataAbsentReason

Short description

Why the component result is missing

Definition

Provides a reason why the expected value in the element Observation.component.value[x] is missing.

Requirements

For many results it is necessary to handle exceptional values in measurements.

Comments

Data type

Binding

Codes specifying why the result (Observation.value[x]) is missing.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1, obs-6

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
v2: N/A
rim: value.nullFlavor

interpretation

0..*

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:variation-code.interpretation

Short description

High, low, normal, etc.

Alternate names

Abnormal Flag

Definition

A categorical assessment of an observation value. For example, high, low, normal.

Requirements

For some results, particularly numeric results, an interpretation is necessary to fully understand the significance of a result.

Comments

Data type

Binding

Codes identifying interpretations of observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
sct-concept: < 260245000 |Findings values|
v2: OBX-8
rim: interpretationCode
sct-attr: 363713009 |Has interpretation|

referenceRange

0..*

There are no (further) constraints on this element

Element id

Observation.component:variation-code.referenceRange

Short description

Provides guide for interpretation of component result

Definition

Guidance on how to interpret the value by comparison to a normal or recommended range.

Requirements

Knowing what values are considered "normal" can help evaluate the significance of a particular result. Need to be able to provide multiple reference ranges for different contexts.

Comments

Mappings

v2: OBX.7
rim: outboundRelationship[typeCode=REFV]/target[classCode=OBS, moodCode=EVN]

chromosome-identifier

S Σ

0..*

There are no (further) constraints on this element

Element id

Observation.component:chromosome-identifier

Short description

Chromosome Identifier

Definition

An indicator, enumerated in humans by numbers 1-22, X, and Y, representing the chromosome on which the variant is located.

Requirements

Comments

For a discussion on the ways Observations can be assembled in groups together see Notes below.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: containment by OBX-4?
rim: outBoundRelationship[typeCode=COMP]

0..1

There are no (further) constraints on this element

Element id

Observation.component:chromosome-identifier.id

Short description

Unique id for inter-element referencing

Definition

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Data type

Mappings

rim: n/a

extension

0..*

There are no (further) constraints on this element

Element id

Observation.component:chromosome-identifier.extension

Short description

Additional content defined by implementations

Alternate names

extensions, user content

Definition

Comments

Data type

Slicing

Unordered, Open, by url(Value)

Extensions are always sliced by (at least) url

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

modifierExtension

Σ ?! C

0..*

There are no (further) constraints on this element

Element id

Observation.component:chromosome-identifier.modifierExtension

Short description

Extensions that cannot be ignored even if unrecognized

Alternate names

extensions, user content, modifiers

Definition

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

Requirements

Comments

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

code

1..1

CodeableConceptPattern

There are no (further) constraints on this element

Element id

Observation.component:chromosome-identifier.code

Short description

48000-4

Definition

Describes what was observed. Sometimes this is called the observation "code".

Requirements

Knowing what kind of observation is being made is essential to understanding the observation.

Comments

All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

Data type

Binding

Codes identifying names of simple observations.

http://loinc.org/vs/LL2938-0 (required)

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Pattern

{
  "coding": [
    {
      "system": "http://loinc.org",
      "code": "48000-4"
    }
  ]
}

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
w5: FiveWs.what[x]
sct-concept: < 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
v2: OBX-3
rim: code

value[x]

1..1

Binding

There are no (further) constraints on this element

Element id

Observation.component:chromosome-identifier.value[x]

Short description

Definition

The information determined as a result of making the observation, if the information has a simple value.

Requirements

An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

Comments

Binding

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
sct-concept: 363714003 |Interprets| < 441742003 |Evaluation finding|
v2: OBX.2, OBX.5, OBX.6
rim: value
sct-attr: 363714003 |Interprets|

valueCodeableConcept

There are no (further) constraints on this element

Data type

dataAbsentReason

0..1

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:chromosome-identifier.dataAbsentReason

Short description

Why the component result is missing

Definition

Provides a reason why the expected value in the element Observation.component.value[x] is missing.

Requirements

For many results it is necessary to handle exceptional values in measurements.

Comments

Data type

Binding

Codes specifying why the result (Observation.value[x]) is missing.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1, obs-6

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
v2: N/A
rim: value.nullFlavor

interpretation

0..*

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:chromosome-identifier.interpretation

Short description

High, low, normal, etc.

Alternate names

Abnormal Flag

Definition

A categorical assessment of an observation value. For example, high, low, normal.

Requirements

For some results, particularly numeric results, an interpretation is necessary to fully understand the significance of a result.

Comments

Data type

Binding

Codes identifying interpretations of observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
sct-concept: < 260245000 |Findings values|
v2: OBX-8
rim: interpretationCode
sct-attr: 363713009 |Has interpretation|

referenceRange

0..*

There are no (further) constraints on this element

Element id

Observation.component:chromosome-identifier.referenceRange

Short description

Provides guide for interpretation of component result

Definition

Guidance on how to interpret the value by comparison to a normal or recommended range.

Requirements

Knowing what values are considered "normal" can help evaluate the significance of a particular result. Need to be able to provide multiple reference ranges for different contexts.

Comments

Mappings

v2: OBX.7
rim: outboundRelationship[typeCode=REFV]/target[classCode=OBS, moodCode=EVN]

protein-hgvs

S Σ

0..1

There are no (further) constraints on this element

Element id

Observation.component:protein-hgvs

Short description

Protein (Amino Acid) Change - pHGVS

Definition

Description of the protein (amino acid) sequence change using a valid HGVS-formatted string. The description of the variant is surrounded in parentheses if it is calculated rather than directly observed.

Requirements

Comments

For a discussion on the ways Observations can be assembled in groups together see Notes below.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: containment by OBX-4?
rim: outBoundRelationship[typeCode=COMP]

0..1

There are no (further) constraints on this element

Element id

Observation.component:protein-hgvs.id

Short description

Unique id for inter-element referencing

Definition

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Data type

Mappings

rim: n/a

extension

0..*

There are no (further) constraints on this element

Element id

Observation.component:protein-hgvs.extension

Short description

Additional content defined by implementations

Alternate names

extensions, user content

Definition

Comments

Data type

Slicing

Unordered, Open, by url(Value)

Extensions are always sliced by (at least) url

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

modifierExtension

Σ ?! C

0..*

There are no (further) constraints on this element

Element id

Observation.component:protein-hgvs.modifierExtension

Short description

Extensions that cannot be ignored even if unrecognized

Alternate names

extensions, user content, modifiers

Definition

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

Requirements

Comments

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

code

1..1

CodeableConceptPattern

There are no (further) constraints on this element

Element id

Observation.component:protein-hgvs.code

Short description

48005-3

Definition

Describes what was observed. Sometimes this is called the observation "code".

Requirements

Knowing what kind of observation is being made is essential to understanding the observation.

Comments

All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

Data type

Binding

Codes identifying names of simple observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Pattern

{
  "coding": [
    {
      "system": "http://loinc.org",
      "code": "48005-3"
    }
  ]
}

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
w5: FiveWs.what[x]
sct-concept: < 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
v2: OBX-3
rim: code

value[x]

1..1

Binding

There are no (further) constraints on this element

Element id

Observation.component:protein-hgvs.value[x]

Short description

A valid HGVS-formatted 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys)

Definition

The information determined as a result of making the observation, if the information has a simple value.

Requirements

An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

Comments

Binding

HGVSVS (required)

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
sct-concept: 363714003 |Interprets| < 441742003 |Evaluation finding|
v2: OBX.2, OBX.5, OBX.6
rim: value
sct-attr: 363714003 |Interprets|

valueCodeableConcept

There are no (further) constraints on this element

Data type

dataAbsentReason

0..1

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:protein-hgvs.dataAbsentReason

Short description

Why the component result is missing

Definition

Provides a reason why the expected value in the element Observation.component.value[x] is missing.

Requirements

For many results it is necessary to handle exceptional values in measurements.

Comments

Data type

Binding

Codes specifying why the result (Observation.value[x]) is missing.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1, obs-6

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
v2: N/A
rim: value.nullFlavor

interpretation

0..*

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:protein-hgvs.interpretation

Short description

High, low, normal, etc.

Alternate names

Abnormal Flag

Definition

A categorical assessment of an observation value. For example, high, low, normal.

Requirements

For some results, particularly numeric results, an interpretation is necessary to fully understand the significance of a result.

Comments

Data type

Binding

Codes identifying interpretations of observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
sct-concept: < 260245000 |Findings values|
v2: OBX-8
rim: interpretationCode
sct-attr: 363713009 |Has interpretation|

referenceRange

0..*

There are no (further) constraints on this element

Element id

Observation.component:protein-hgvs.referenceRange

Short description

Provides guide for interpretation of component result

Definition

Guidance on how to interpret the value by comparison to a normal or recommended range.

Requirements

Knowing what values are considered "normal" can help evaluate the significance of a particular result. Need to be able to provide multiple reference ranges for different contexts.

Comments

Mappings

v2: OBX.7
rim: outboundRelationship[typeCode=REFV]/target[classCode=OBS, moodCode=EVN]

amino-acid-change-type

S Σ

0..1

There are no (further) constraints on this element

Element id

Observation.component:amino-acid-change-type

Short description

Amino Acid Change Type

Definition

Codified type for associated Amino Acid Marker, for convenience.

Requirements

Comments

For a discussion on the ways Observations can be assembled in groups together see Notes below.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: containment by OBX-4?
rim: outBoundRelationship[typeCode=COMP]

0..1

There are no (further) constraints on this element

Element id

Observation.component:amino-acid-change-type.id

Short description

Unique id for inter-element referencing

Definition

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Data type

Mappings

rim: n/a

extension

0..*

There are no (further) constraints on this element

Element id

Observation.component:amino-acid-change-type.extension

Short description

Additional content defined by implementations

Alternate names

extensions, user content

Definition

Comments

Data type

Slicing

Unordered, Open, by url(Value)

Extensions are always sliced by (at least) url

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

modifierExtension

Σ ?! C

0..*

There are no (further) constraints on this element

Element id

Observation.component:amino-acid-change-type.modifierExtension

Short description

Extensions that cannot be ignored even if unrecognized

Alternate names

extensions, user content, modifiers

Definition

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

Requirements

Comments

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

code

1..1

CodeableConceptPattern

There are no (further) constraints on this element

Element id

Observation.component:amino-acid-change-type.code

Short description

48006-1

Definition

Describes what was observed. Sometimes this is called the observation "code".

Requirements

Knowing what kind of observation is being made is essential to understanding the observation.

Comments

All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

Data type

Binding

Codes identifying names of simple observations.

http://loinc.org/vs/LL380-7 (extensible)

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Pattern

{
  "coding": [
    {
      "system": "http://loinc.org",
      "code": "48006-1"
    }
  ]
}

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
w5: FiveWs.what[x]
sct-concept: < 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
v2: OBX-3
rim: code

value[x]

1..1

Binding

There are no (further) constraints on this element

Element id

Observation.component:amino-acid-change-type.value[x]

Short description

Definition

The information determined as a result of making the observation, if the information has a simple value.

Requirements

An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

Comments

Binding

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
sct-concept: 363714003 |Interprets| < 441742003 |Evaluation finding|
v2: OBX.2, OBX.5, OBX.6
rim: value
sct-attr: 363714003 |Interprets|

valueCodeableConcept

There are no (further) constraints on this element

Data type

dataAbsentReason

0..1

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:amino-acid-change-type.dataAbsentReason

Short description

Why the component result is missing

Definition

Provides a reason why the expected value in the element Observation.component.value[x] is missing.

Requirements

For many results it is necessary to handle exceptional values in measurements.

Comments

Data type

Binding

Codes specifying why the result (Observation.value[x]) is missing.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1, obs-6

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
v2: N/A
rim: value.nullFlavor

interpretation

0..*

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:amino-acid-change-type.interpretation

Short description

High, low, normal, etc.

Alternate names

Abnormal Flag

Definition

A categorical assessment of an observation value. For example, high, low, normal.

Requirements

For some results, particularly numeric results, an interpretation is necessary to fully understand the significance of a result.

Comments

Data type

Binding

Codes identifying interpretations of observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
sct-concept: < 260245000 |Findings values|
v2: OBX-8
rim: interpretationCode
sct-attr: 363713009 |Has interpretation|

referenceRange

0..*

There are no (further) constraints on this element

Element id

Observation.component:amino-acid-change-type.referenceRange

Short description

Provides guide for interpretation of component result

Definition

Guidance on how to interpret the value by comparison to a normal or recommended range.

Requirements

Knowing what values are considered "normal" can help evaluate the significance of a particular result. Need to be able to provide multiple reference ranges for different contexts.

Comments

Mappings

v2: OBX.7
rim: outboundRelationship[typeCode=REFV]/target[classCode=OBS, moodCode=EVN]

molecular-consequence

S Σ

0..1

There are no (further) constraints on this element

Element id

Observation.component:molecular-consequence

Short description

Molecular Consequence

Definition

The calculated or observed effect of a variant on its downstream transcript and, if applicable, ensuing protein sequence.

Requirements

Comments

For a discussion on the ways Observations can be assembled in groups together see Notes below.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: containment by OBX-4?
rim: outBoundRelationship[typeCode=COMP]

0..1

There are no (further) constraints on this element

Element id

Observation.component:molecular-consequence.id

Short description

Unique id for inter-element referencing

Definition

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Data type

Mappings

rim: n/a

extension

0..*

There are no (further) constraints on this element

Element id

Observation.component:molecular-consequence.extension

Short description

Additional content defined by implementations

Alternate names

extensions, user content

Definition

Comments

Data type

Slicing

Unordered, Open, by url(Value)

Extensions are always sliced by (at least) url

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

modifierExtension

Σ ?! C

0..*

There are no (further) constraints on this element

Element id

Observation.component:molecular-consequence.modifierExtension

Short description

Extensions that cannot be ignored even if unrecognized

Alternate names

extensions, user content, modifiers

Definition

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

Requirements

Comments

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

code

1..1

CodeableConceptPattern

There are no (further) constraints on this element

Element id

Observation.component:molecular-consequence.code

Short description

molecular-consequence

Definition

Describes what was observed. Sometimes this is called the observation "code".

Requirements

Knowing what kind of observation is being made is essential to understanding the observation.

Comments

All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

Data type

Binding

Codes identifying names of simple observations.

MolecularConsequenceVS (extensible)

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Pattern

{
  "coding": [
    {
      "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
      "code": "molecular-consequence"
    }
  ]
}

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
w5: FiveWs.what[x]
sct-concept: < 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
v2: OBX-3
rim: code

value[x]

1..1

Binding

There are no (further) constraints on this element

Element id

Observation.component:molecular-consequence.value[x]

Short description

stop_lost | stop_gained | inframe_insertion | frameshift_variant | ... (many)

Definition

The information determined as a result of making the observation, if the information has a simple value.

Requirements

An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

Comments

Binding

Concepts in sequence ontology under SO:0001537.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
sct-concept: 363714003 |Interprets| < 441742003 |Evaluation finding|
v2: OBX.2, OBX.5, OBX.6
rim: value
sct-attr: 363714003 |Interprets|

valueCodeableConcept

There are no (further) constraints on this element

Data type

dataAbsentReason

0..1

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:molecular-consequence.dataAbsentReason

Short description

Why the component result is missing

Definition

Provides a reason why the expected value in the element Observation.component.value[x] is missing.

Requirements

For many results it is necessary to handle exceptional values in measurements.

Comments

Data type

Binding

Codes specifying why the result (Observation.value[x]) is missing.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1, obs-6

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
v2: N/A
rim: value.nullFlavor

interpretation

0..*

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:molecular-consequence.interpretation

Short description

High, low, normal, etc.

Alternate names

Abnormal Flag

Definition

A categorical assessment of an observation value. For example, high, low, normal.

Requirements

For some results, particularly numeric results, an interpretation is necessary to fully understand the significance of a result.

Comments

Data type

Binding

Codes identifying interpretations of observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
sct-concept: < 260245000 |Findings values|
v2: OBX-8
rim: interpretationCode
sct-attr: 363713009 |Has interpretation|

referenceRange

0..*

There are no (further) constraints on this element

Element id

Observation.component:molecular-consequence.referenceRange

Short description

Provides guide for interpretation of component result

Definition

Guidance on how to interpret the value by comparison to a normal or recommended range.

Requirements

Knowing what values are considered "normal" can help evaluate the significance of a particular result. Need to be able to provide multiple reference ranges for different contexts.

Comments

Mappings

v2: OBX.7
rim: outboundRelationship[typeCode=REFV]/target[classCode=OBS, moodCode=EVN]

copy-number

S Σ

0..1

There are no (further) constraints on this element

Element id

Observation.component:copy-number

Short description

Genomic Structural Variant Copy Number

Definition

The copy number of the large variant. In HGVS, this is the numeric value following the “X”. It is a unit-less value. Note that a copy number of 1 can imply a deletion.

Requirements

Comments

For a discussion on the ways Observations can be assembled in groups together see Notes below.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: containment by OBX-4?
rim: outBoundRelationship[typeCode=COMP]

0..1

There are no (further) constraints on this element

Element id

Observation.component:copy-number.id

Short description

Unique id for inter-element referencing

Definition

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Data type

Mappings

rim: n/a

extension

0..*

There are no (further) constraints on this element

Element id

Observation.component:copy-number.extension

Short description

Additional content defined by implementations

Alternate names

extensions, user content

Definition

Comments

Data type

Slicing

Unordered, Open, by url(Value)

Extensions are always sliced by (at least) url

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

modifierExtension

Σ ?! C

0..*

There are no (further) constraints on this element

Element id

Observation.component:copy-number.modifierExtension

Short description

Extensions that cannot be ignored even if unrecognized

Alternate names

extensions, user content, modifiers

Definition

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

Requirements

Comments

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

code

1..1

CodeableConceptPattern

There are no (further) constraints on this element

Element id

Observation.component:copy-number.code

Short description

82155-3

Definition

Describes what was observed. Sometimes this is called the observation "code".

Requirements

Knowing what kind of observation is being made is essential to understanding the observation.

Comments

All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

Data type

Binding

Codes identifying names of simple observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Pattern

{
  "coding": [
    {
      "system": "http://loinc.org",
      "code": "82155-3"
    }
  ]
}

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
w5: FiveWs.what[x]
sct-concept: < 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
v2: OBX-3
rim: code

value[x]

Σ C

0..1

There are no (further) constraints on this element

Element id

Observation.component:copy-number.value[x]

Short description

Actual component result

Definition

The information determined as a result of making the observation, if the information has a simple value.

Requirements

An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

Comments

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
cnt-3: There SHALL be a code with a value of '1' if there is a value. If system is present, it SHALL be UCUM. If present, the value SHALL be a whole number.
(code.exists() or value.empty()) and (system.empty() or system = %ucum) and (code.empty() or code = '1') and (value.empty() or value.hasValue().not() or value.toString().contains('.').not())

Mappings

rim: n/a
sct-concept: 363714003 |Interprets| < 441742003 |Evaluation finding|
v2: OBX.2, OBX.5, OBX.6
rim: value
sct-attr: 363714003 |Interprets|

valueQuantity

There are no (further) constraints on this element

Data type

dataAbsentReason

0..1

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:copy-number.dataAbsentReason

Short description

Why the component result is missing

Definition

Provides a reason why the expected value in the element Observation.component.value[x] is missing.

Requirements

For many results it is necessary to handle exceptional values in measurements.

Comments

Data type

Binding

Codes specifying why the result (Observation.value[x]) is missing.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1, obs-6

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
v2: N/A
rim: value.nullFlavor

interpretation

0..*

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:copy-number.interpretation

Short description

High, low, normal, etc.

Alternate names

Abnormal Flag

Definition

A categorical assessment of an observation value. For example, high, low, normal.

Requirements

For some results, particularly numeric results, an interpretation is necessary to fully understand the significance of a result.

Comments

Data type

Binding

Codes identifying interpretations of observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
sct-concept: < 260245000 |Findings values|
v2: OBX-8
rim: interpretationCode
sct-attr: 363713009 |Has interpretation|

referenceRange

0..*

There are no (further) constraints on this element

Element id

Observation.component:copy-number.referenceRange

Short description

Provides guide for interpretation of component result

Definition

Guidance on how to interpret the value by comparison to a normal or recommended range.

Requirements

Knowing what values are considered "normal" can help evaluate the significance of a particular result. Need to be able to provide multiple reference ranges for different contexts.

Comments

Mappings

v2: OBX.7
rim: outboundRelationship[typeCode=REFV]/target[classCode=OBS, moodCode=EVN]

variant-confidence-status

S Σ

0..1

There are no (further) constraints on this element

Element id

Observation.component:variant-confidence-status

Short description

Variant Confidence Status

Definition

A code that represents the confidence of a true positive variant call.

Requirements

Comments

For a discussion on the ways Observations can be assembled in groups together see Notes below.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: containment by OBX-4?
rim: outBoundRelationship[typeCode=COMP]

0..1

There are no (further) constraints on this element

Element id

Observation.component:variant-confidence-status.id

Short description

Unique id for inter-element referencing

Definition

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Data type

Mappings

rim: n/a

extension

0..*

There are no (further) constraints on this element

Element id

Observation.component:variant-confidence-status.extension

Short description

Additional content defined by implementations

Alternate names

extensions, user content

Definition

Comments

Data type

Slicing

Unordered, Open, by url(Value)

Extensions are always sliced by (at least) url

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

modifierExtension

Σ ?! C

0..*

There are no (further) constraints on this element

Element id

Observation.component:variant-confidence-status.modifierExtension

Short description

Extensions that cannot be ignored even if unrecognized

Alternate names

extensions, user content, modifiers

Definition

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

Requirements

Comments

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

code

1..1

CodeableConceptPattern

There are no (further) constraints on this element

Element id

Observation.component:variant-confidence-status.code

Short description

variant-confidence-status

Definition

Describes what was observed. Sometimes this is called the observation "code".

Requirements

Knowing what kind of observation is being made is essential to understanding the observation.

Comments

All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

Data type

Binding

Codes identifying names of simple observations.

VariantConfidenceStatusVS (required)

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Pattern

{
  "coding": [
    {
      "system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
      "code": "variant-confidence-status"
    }
  ]
}

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
w5: FiveWs.what[x]
sct-concept: < 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
v2: OBX-3
rim: code

value[x]

1..1

Binding

There are no (further) constraints on this element

Element id

Observation.component:variant-confidence-status.value[x]

Short description

High | Intermediate | Low

Definition

The information determined as a result of making the observation, if the information has a simple value.

Requirements

An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

Comments

Binding

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
sct-concept: 363714003 |Interprets| < 441742003 |Evaluation finding|
v2: OBX.2, OBX.5, OBX.6
rim: value
sct-attr: 363714003 |Interprets|

valueCodeableConcept

There are no (further) constraints on this element

Data type

dataAbsentReason

0..1

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:variant-confidence-status.dataAbsentReason

Short description

Why the component result is missing

Definition

Provides a reason why the expected value in the element Observation.component.value[x] is missing.

Requirements

For many results it is necessary to handle exceptional values in measurements.

Comments

Data type

Binding

Codes specifying why the result (Observation.value[x]) is missing.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1, obs-6

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
v2: N/A
rim: value.nullFlavor

interpretation

0..*

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:variant-confidence-status.interpretation

Short description

High, low, normal, etc.

Alternate names

Abnormal Flag

Definition

A categorical assessment of an observation value. For example, high, low, normal.

Requirements

For some results, particularly numeric results, an interpretation is necessary to fully understand the significance of a result.

Comments

Data type

Binding

Codes identifying interpretations of observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
sct-concept: < 260245000 |Findings values|
v2: OBX-8
rim: interpretationCode
sct-attr: 363713009 |Has interpretation|

referenceRange

0..*

There are no (further) constraints on this element

Element id

Observation.component:variant-confidence-status.referenceRange

Short description

Provides guide for interpretation of component result

Definition

Guidance on how to interpret the value by comparison to a normal or recommended range.

Requirements

Knowing what values are considered "normal" can help evaluate the significance of a particular result. Need to be able to provide multiple reference ranges for different contexts.

Comments

Mappings

v2: OBX.7
rim: outboundRelationship[typeCode=REFV]/target[classCode=OBS, moodCode=EVN]

dna-region

S Σ

0..*

There are no (further) constraints on this element

Element id

Observation.component:dna-region

Short description

DNA region name [Identifier]

Definition

A human readable name for the region of interest. Typically Exon #, Intron # or other.

Requirements

Comments

For a discussion on the ways Observations can be assembled in groups together see Notes below.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: containment by OBX-4?
rim: outBoundRelationship[typeCode=COMP]

0..1

There are no (further) constraints on this element

Element id

Observation.component:dna-region.id

Short description

Unique id for inter-element referencing

Definition

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Data type

Mappings

rim: n/a

extension

0..*

There are no (further) constraints on this element

Element id

Observation.component:dna-region.extension

Short description

Additional content defined by implementations

Alternate names

extensions, user content

Definition

Comments

Data type

Slicing

Unordered, Open, by url(Value)

Extensions are always sliced by (at least) url

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

modifierExtension

Σ ?! C

0..*

There are no (further) constraints on this element

Element id

Observation.component:dna-region.modifierExtension

Short description

Extensions that cannot be ignored even if unrecognized

Alternate names

extensions, user content, modifiers

Definition

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

Requirements

Comments

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

code

1..1

CodeableConceptPattern

There are no (further) constraints on this element

Element id

Observation.component:dna-region.code

Short description

47999-8

Definition

Describes what was observed. Sometimes this is called the observation "code".

Requirements

Knowing what kind of observation is being made is essential to understanding the observation.

Comments

All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

Data type

Binding

Codes identifying names of simple observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Pattern

{
  "coding": [
    {
      "system": "http://loinc.org",
      "code": "47999-8"
    }
  ]
}

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
w5: FiveWs.what[x]
sct-concept: < 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
v2: OBX-3
rim: code

value[x]

1..1

There are no (further) constraints on this element

Element id

Observation.component:dna-region.value[x]

Short description

Actual component result

Definition

The information determined as a result of making the observation, if the information has a simple value.

Requirements

An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

Comments

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
sct-concept: 363714003 |Interprets| < 441742003 |Evaluation finding|
v2: OBX.2, OBX.5, OBX.6
rim: value
sct-attr: 363714003 |Interprets|

valueString

There are no (further) constraints on this element

Data type

dataAbsentReason

0..1

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:dna-region.dataAbsentReason

Short description

Why the component result is missing

Definition

Provides a reason why the expected value in the element Observation.component.value[x] is missing.

Requirements

For many results it is necessary to handle exceptional values in measurements.

Comments

Data type

Binding

Codes specifying why the result (Observation.value[x]) is missing.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1, obs-6

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
v2: N/A
rim: value.nullFlavor

interpretation

0..*

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:dna-region.interpretation

Short description

High, low, normal, etc.

Alternate names

Abnormal Flag

Definition

A categorical assessment of an observation value. For example, high, low, normal.

Requirements

For some results, particularly numeric results, an interpretation is necessary to fully understand the significance of a result.

Comments

Data type

Binding

Codes identifying interpretations of observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
sct-concept: < 260245000 |Findings values|
v2: OBX-8
rim: interpretationCode
sct-attr: 363713009 |Has interpretation|

referenceRange

0..*

There are no (further) constraints on this element

Element id

Observation.component:dna-region.referenceRange

Short description

Provides guide for interpretation of component result

Definition

Guidance on how to interpret the value by comparison to a normal or recommended range.

Requirements

Knowing what values are considered "normal" can help evaluate the significance of a particular result. Need to be able to provide multiple reference ranges for different contexts.

Comments

Mappings

v2: OBX.7
rim: outboundRelationship[typeCode=REFV]/target[classCode=OBS, moodCode=EVN]

gene-fusion

S Σ

0..1

There are no (further) constraints on this element

Element id

Observation.component:gene-fusion

Short description

Gene fusion transcript details in Blood or Tissue by Molecular genetics method Narrative

Definition

Requirements

Comments

For a discussion on the ways Observations can be assembled in groups together see Notes below.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: containment by OBX-4?
rim: outBoundRelationship[typeCode=COMP]

0..1

There are no (further) constraints on this element

Element id

Observation.component:gene-fusion.id

Short description

Unique id for inter-element referencing

Definition

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Data type

Mappings

rim: n/a

extension

0..*

There are no (further) constraints on this element

Element id

Observation.component:gene-fusion.extension

Short description

Additional content defined by implementations

Alternate names

extensions, user content

Definition

Comments

Data type

Slicing

Unordered, Open, by url(Value)

Extensions are always sliced by (at least) url

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

modifierExtension

Σ ?! C

0..*

There are no (further) constraints on this element

Element id

Observation.component:gene-fusion.modifierExtension

Short description

Extensions that cannot be ignored even if unrecognized

Alternate names

extensions, user content, modifiers

Definition

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

Requirements

Comments

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

code

1..1

CodeableConceptPattern

There are no (further) constraints on this element

Element id

Observation.component:gene-fusion.code

Short description

Type of component observation (code / type)

Definition

Describes what was observed. Sometimes this is called the observation "code".

Requirements

Knowing what kind of observation is being made is essential to understanding the observation.

Comments

All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

Data type

Binding

Codes identifying names of simple observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Pattern

{
  "coding": [
    {
      "system": "http://loinc.org",
      "code": "95123-6"
    }
  ]
}

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
w5: FiveWs.what[x]
sct-concept: < 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
v2: OBX-3
rim: code

value[x]

1..1

Binding

There are no (further) constraints on this element

Element id

Observation.component:gene-fusion.value[x]

Short description

HGNC recommends for products of gene translocations or fusions (format GENESYMBOL1::GENESYMBOL2) and readthrough transcripts (format GENESYMBOL1-GENESYMBOL2)

Definition

The information determined as a result of making the observation, if the information has a simple value.

Requirements

An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

Comments

Binding

HGNCVS (extensible)

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
sct-concept: 363714003 |Interprets| < 441742003 |Evaluation finding|
v2: OBX.2, OBX.5, OBX.6
rim: value
sct-attr: 363714003 |Interprets|

valueCodeableConcept

There are no (further) constraints on this element

Data type

dataAbsentReason

0..1

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:gene-fusion.dataAbsentReason

Short description

Why the component result is missing

Definition

Provides a reason why the expected value in the element Observation.component.value[x] is missing.

Requirements

For many results it is necessary to handle exceptional values in measurements.

Comments

Data type

Binding

Codes specifying why the result (Observation.value[x]) is missing.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1, obs-6

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
v2: N/A
rim: value.nullFlavor

interpretation

0..*

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:gene-fusion.interpretation

Short description

High, low, normal, etc.

Alternate names

Abnormal Flag

Definition

A categorical assessment of an observation value. For example, high, low, normal.

Requirements

For some results, particularly numeric results, an interpretation is necessary to fully understand the significance of a result.

Comments

Data type

Binding

Codes identifying interpretations of observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
sct-concept: < 260245000 |Findings values|
v2: OBX-8
rim: interpretationCode
sct-attr: 363713009 |Has interpretation|

referenceRange

0..*

There are no (further) constraints on this element

Element id

Observation.component:gene-fusion.referenceRange

Short description

Provides guide for interpretation of component result

Definition

Guidance on how to interpret the value by comparison to a normal or recommended range.

Requirements

Knowing what values are considered "normal" can help evaluate the significance of a particular result. Need to be able to provide multiple reference ranges for different contexts.

Comments

Mappings

v2: OBX.7
rim: outboundRelationship[typeCode=REFV]/target[classCode=OBS, moodCode=EVN]

detection-limit

S Σ

0..1

There are no (further) constraints on this element

Element id

Observation.component:detection-limit

Short description

Laboratory device Detection limit

Definition

Requirements

Comments

For a discussion on the ways Observations can be assembled in groups together see Notes below.

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: containment by OBX-4?
rim: outBoundRelationship[typeCode=COMP]

0..1

There are no (further) constraints on this element

Element id

Observation.component:detection-limit.id

Short description

Unique id for inter-element referencing

Definition

Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.

Data type

Mappings

rim: n/a

extension

0..*

There are no (further) constraints on this element

Element id

Observation.component:detection-limit.extension

Short description

Additional content defined by implementations

Alternate names

extensions, user content

Definition

Comments

Data type

Slicing

Unordered, Open, by url(Value)

Extensions are always sliced by (at least) url

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

modifierExtension

Σ ?! C

0..*

There are no (further) constraints on this element

Element id

Observation.component:detection-limit.modifierExtension

Short description

Extensions that cannot be ignored even if unrecognized

Alternate names

extensions, user content, modifiers

Definition

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

Requirements

Comments

Data type

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())
ext-1: Must have either extensions or value[x], not both
extension.exists() != value.exists()

Mappings

rim: n/a
rim: N/A

code

1..1

CodeableConceptPattern

There are no (further) constraints on this element

Element id

Observation.component:detection-limit.code

Short description

Type of component observation (code / type)

Definition

Describes what was observed. Sometimes this is called the observation "code".

Requirements

Knowing what kind of observation is being made is essential to understanding the observation.

Comments

All code-value and component.code-component.value pairs need to be taken into account to correctly understand the meaning of the observation.

Data type

Binding

Codes identifying names of simple observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Pattern

{
  "coding": [
    {
      "system": "http://loinc.org",
      "code": "87706-8"
    }
  ]
}

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
w5: FiveWs.what[x]
sct-concept: < 363787002 |Observable entity| OR < 386053000 |Evaluation procedure|
v2: OBX-3
rim: code

value[x]

0..1

There are no (further) constraints on this element

Element id

Observation.component:detection-limit.value[x]

Short description

Usually reported as percentage.

Definition

The information determined as a result of making the observation, if the information has a simple value.

Requirements

An observation exists to have a value, though it might not if it is in error, or if it represents a group of observations.

Comments

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
sct-concept: 363714003 |Interprets| < 441742003 |Evaluation finding|
v2: OBX.2, OBX.5, OBX.6
rim: value
sct-attr: 363714003 |Interprets|

valueQuantity

There are no (further) constraints on this element

Data type

dataAbsentReason

0..1

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:detection-limit.dataAbsentReason

Short description

Why the component result is missing

Definition

Provides a reason why the expected value in the element Observation.component.value[x] is missing.

Requirements

For many results it is necessary to handle exceptional values in measurements.

Comments

Data type

Binding

Codes specifying why the result (Observation.value[x]) is missing.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1, obs-6

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
v2: N/A
rim: value.nullFlavor

interpretation

0..*

CodeableConceptBinding

There are no (further) constraints on this element

Element id

Observation.component:detection-limit.interpretation

Short description

High, low, normal, etc.

Alternate names

Abnormal Flag

Definition

A categorical assessment of an observation value. For example, high, low, normal.

Requirements

For some results, particularly numeric results, an interpretation is necessary to fully understand the significance of a result.

Comments

Data type

Binding

Codes identifying interpretations of observations.

Conditions

The cardinality or value of this element may be affected by these constraints: ele-1

Constraints

ele-1: All FHIR elements must have a @value or children
hasValue() or (children().count() > id.count())

Mappings

rim: n/a
v2: CE/CNE/CWE
rim: CD
orim: fhir:CodeableConcept rdfs:subClassOf dt:CD
sct-concept: < 260245000 |Findings values|
v2: OBX-8
rim: interpretationCode
sct-attr: 363713009 |Has interpretation|

referenceRange

0..*